# Copyright 2020 by Michiel de Hoon. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for Bio.Align.hhr module.""" import os import unittest import numpy as np from Bio import Align class Align_hhr_2uvo_hhblits(unittest.TestCase): path = os.path.join("HHsuite", "2uvo_hhblits.hhr") def test_reading(self): alignments = Align.parse(self.path, "hhr") self.check_alignments(alignments) alignments = iter(alignments) self.check_alignments(alignments) with Align.parse(self.path, "hhr") as alignments: self.check_alignments(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(self.path, "hhr") as alignments: pass with self.assertRaises(AttributeError): alignments._stream def check_alignments(self, alignments): self.assertEqual(alignments.metadata["No_of_seqs"], (1560, 4005)) self.assertAlmostEqual(alignments.metadata["Neff"], 8.3) self.assertEqual(alignments.metadata["Searched_HMMs"], 34) self.assertEqual(alignments.metadata["Rundate"], "Fri Feb 15 16:34:13 2019") self.assertEqual( alignments.metadata["Command line"], "hhblits -i 2uvoAh.fasta -d /pdb70" ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.95) self.assertAlmostEqual(alignment.annotations["E-value"], 3.7e-34, places=35) self.assertAlmostEqual(alignment.annotations["Score"], 210.31) self.assertAlmostEqual(alignment.annotations["Identities"], 100) self.assertAlmostEqual(alignment.annotations["Similarity"], 2.050) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 166.9) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:171], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG", ) self.assertEqual( alignment[1], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~c~~~~~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~~c~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~gCq~~~c~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~~cg~~~~~~~c~~~~CCS~~g~Cg~~~~~Cg~gC~~~~c~~~~~cg~~~~~~~c~~~~CCs~~g~Cg~~~~~c~~~c~~~~~~~~~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~C~~gCq~~~c~~~~~cg~~~~~~~c~~~~ccs~~g~Cg~~~~~C~~~cq~~~~~~", ) self.assertEqual(alignment.target.id, "2uvo_A") self.assertEqual( alignment.target.seq[0:171], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG", ) self.assertEqual(alignment.target.annotations["hmm_name"], "2uvo_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Agglutinin isolectin 1; carbohydrate-binding protein, hevein domain, chitin-binding, GERM agglutinin, chitin-binding protein; HET: NDG NAG GOL; 1.40A {Triticum aestivum} PDB: 1wgc_A* 2cwg_A* 2x3t_A* 4aml_A* 7wga_A 9wga_A 2wgc_A 1wgt_A 1k7t_A* 1k7v_A* 1k7u_A 2x52_A* 1t0w_A*", ) self.assertEqual( alignment[0], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CBCBGGGTTBBCGGGCEECTTSBEEBSHHHHSTTCCBSSCSSCCBCBGGGTTBCCSTTCEECTTSBEEBSHHHHSTTCCBSSCSSCCBCBGGGTTBCCGGGCEECTTSBEEBSHHHHSTTCCBSSCSSCCCCBTTTTTBCCSTTCEECTTSCEEBSHHHHSTTCCBSSCC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCCCCCCCCcCCCCCCeeCCCCeECCCcccccCCccccccccccccCcccCCcccCCccccCCCceeCCCccccCCCcccccccccccccccccCCCCCCCcccCCCCccCCCcccccCCCcCCccccccccccccccccCCCCCCcCCCCEecCchhhcccccccCCCCC", ) self.assertEqual( alignment.column_annotations["Confidence"], "799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999998899999999999999999999999999999999999999999999999999999999999999999999999999986", ) self.assertEqual( str(alignment), """\ 2uvo_A 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQC 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 2UVO:A|PD 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQC 2uvo_A 60 CSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 2UVO:A|PD 60 CSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG 2uvo_A 120 CQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171 120 ||||||||||||||||||||||||||||||||||||||||||||||||||| 171 2UVO:A|PD 120 CQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 171], [ 0, 171]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G', 'G', 'C', 'D', 'G'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G', 'G', 'C', 'D', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.92) self.assertAlmostEqual(alignment.annotations["E-value"], 1.1e-30, places=31) self.assertAlmostEqual(alignment.annotations["Score"], 190.44) self.assertAlmostEqual(alignment.annotations["Identities"], 49) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.254) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 148.8) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:169], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC", ) self.assertEqual( alignment[1], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~c~~~~~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~~c~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~gCq~~~c ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~g~~~~~~~c~~~~CCs~~g~Cg~~~~~c~~~C~~~~c~~~~~cg~~~~~c~~~~CCs~~G~CG~~~~~C~~~C~~~~~~~~~~Cg~~~~~c~~~~Ccs~~G~CGt~~~~C~~~cq~~~c~~~~~cg~~~~~c~~~~Ccs~~g~Cg~~~~~C~~~cq~~~~ ", ) self.assertEqual(alignment.target.id, "2wga") self.assertEqual( alignment.target.seq[1:163], "GXGCXGXXMYCSTNNCCXXWESCGSGGYXCGEGCNLGACQXGXPCXXPGSVCTNLHCCARGGHCGMGSGYCGXGCXGGACXADIXCGXGXXXCPTDSCCGGWGXCGNGXEFCGXGCXVGGCAAXSPCGXPGSXCTLDKCCSGXGACXSGSGGCGXGCXAGGC", ) self.assertEqual(alignment.target.annotations["hmm_name"], "2wga") self.assertEqual( alignment.target.annotations["hmm_description"], "; lectin (agglutinin); NMR {}", ) self.assertEqual( alignment[0], "GXGCXGXXMYCSTNNCCXXWESCGSGGYXCGEGCNLGACQXGXPCXX--PGSVCTNLHCCARGGHCGMGSGYCGXGCXGGACXADIXCGXG--XXXCPTDSCCGGWGXCGNGXEFCGXGCXVGGCAAXSPCGXP--GSXCTLDKCCSGXGACXSGSGGCGXGCXAGGC", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSGGGSSCCCCSTTCEECTTSCEECSTTTTSTTCCSSSCSSCCCSSSSSCCCSTTCEECTTSCEESSHHHHSSCCSSSSCSSCCCCTTSSSCCSTTCBCCSSSCCBCSHHHHSTTCCSSSCSSCCCCSSSCCCCSTTCEECSSSSEECSTTTTSSCCSSSSC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ccCCCcccccCCCCceECCcceECCCCccccCccccCcccccceeccCCCcCCCCcccCCCceeCCCCcccCCCccccccccccccCcccccCCCCCccCCCCCccCccccccCCccccccccccccCCCcccCCcccccCCCCceeCCccccCCCCcCCCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 699999999999999999999999999999999999888888899873567889999999999999999999999988888888999744568899999999999999999999999999998899987356788999999999999999999999999876 ", ) self.assertEqual( str(alignment), """\ 2wga 1 GXGCXGXXMYCSTNNCCXXWESCGSGGYXCGEGCNLGACQXGXPCXX--PGSVCTNLHCC 0 ..|..|..|.|..|.||.....||.||..||.||..|||.....|..--.|..|||..|| 2UVO:A|PD 1 RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCC 2wga 59 ARGGHCGMGSGYCGXGCXGGACXADIXCGXG--XXXCPTDSCCGGWGXCGNGXEFCGXGC 60 ...|.||.|..|||.||.||.|.|||.||..--...||...||..||.||.|.||||.|| 2UVO:A|PD 61 SQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGC 2wga 117 XVGGCAAXSPCGXP--GSXCTLDKCCSGXGACXSGSGGCGXGCXAGGC 163 120 ..|.|....|||..--|..||...|||..|.|..|.|.||.||..||| 168 2UVO:A|PD 121 QSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC 169 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 48, 48, 90, 90, 131, 131, 163], [ 1, 48, 50, 92, 94, 135, 137, 169]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'X', 'G', 'C', 'X', 'G', 'X', 'X', 'M', 'Y', 'C', 'S', 'T', 'N', 'N', 'C', 'C', 'X', 'X', 'W', 'E', 'S', 'C', 'G', 'S', 'G', 'G', 'Y', 'X', 'C', 'G', 'E', 'G', 'C', 'N', 'L', 'G', 'A', 'C', 'Q', 'X', 'G', 'X', 'P', 'C', 'X', 'X', '-', '-', 'P', 'G', 'S', 'V', 'C', 'T', 'N', 'L', 'H', 'C', 'C', 'A', 'R', 'G', 'G', 'H', 'C', 'G', 'M', 'G', 'S', 'G', 'Y', 'C', 'G', 'X', 'G', 'C', 'X', 'G', 'G', 'A', 'C', 'X', 'A', 'D', 'I', 'X', 'C', 'G', 'X', 'G', '-', '-', 'X', 'X', 'X', 'C', 'P', 'T', 'D', 'S', 'C', 'C', 'G', 'G', 'W', 'G', 'X', 'C', 'G', 'N', 'G', 'X', 'E', 'F', 'C', 'G', 'X', 'G', 'C', 'X', 'V', 'G', 'G', 'C', 'A', 'A', 'X', 'S', 'P', 'C', 'G', 'X', 'P', '-', '-', 'G', 'S', 'X', 'C', 'T', 'L', 'D', 'K', 'C', 'C', 'S', 'G', 'X', 'G', 'A', 'C', 'X', 'S', 'G', 'S', 'G', 'G', 'C', 'G', 'X', 'G', 'C', 'X', 'A', 'G', 'G', 'C'], ['R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G', 'G', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.77) self.assertAlmostEqual(alignment.annotations["E-value"], 5.2e-24, places=25) self.assertAlmostEqual(alignment.annotations["Score"], 148.19) self.assertAlmostEqual(alignment.annotations["Identities"], 50) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.303) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 103.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:124], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG", ) self.assertEqual( alignment[1], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~c~~~~~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~cg~~~~~~~c~~g~CCs~~g~CG~~~~~Cg~gCq~~c~~~~Cg~~~~~~~c~~~~CCs~~G~CG~~~~~C~~~Cq~~c~~~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~C~~gCq~~ ", ) self.assertEqual(alignment.target.id, "1ulk_A") self.assertEqual( alignment.target.seq[1:121], "PVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQCDYNRCGKEFGGKECHDELCCSQYGWCGNSDGHCGEGCQSQCSYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDGCQSQ", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1ulk_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Lectin-C; chitin-binding protein, hevein domain, PL-C, sugar binding protein; 1.80A {Phytolacca americana} SCOP: g.3.1.1 g.3.1.1 g.3.1.1", ) self.assertEqual( alignment[0], "PVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQ-C-DYNRCGKEFGGKECHDELCCSQYGWCGNSDGHCGEGCQSQ-C-SYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDGCQSQ", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCSBGGGTTBCCGGGCEECTTSCEESSHHHHSTTCCBCTTTTBCBGGGTTBCCGGGCEECTTSBEECSHHHHSTTCCBCTTTTBCBGGGTTBCCSTTCEECTTSBEECSHHHHSTTCCBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CcCcCCCCCCCCCCCCeECCCCeeCCCccccCCCccccceeeeccccccCCCCCCccccCCCcccccCcccccCCcccccCcccccccCCCccCCCCcccccCceecCcccccCcccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 389999999999999999999999999999999999752346788765567888999999999999999999999986422467877554567899999999999999999999999973 ", ) self.assertEqual( str(alignment), """\ 1ulk_A 1 PVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQ-C-DYNRCGKEFGGKECHDELC 0 ..||...|...||...||||.||||....|||||||..-|-...|||...||..|....| 2UVO:A|PD 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQC 1ulk_A 59 CSQYGWCGNSDGHCGEGCQSQ-C-SYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDG 60 |||||.||.....||.|||..-|-....||...||.||....||||.|.|||....|..| 2UVO:A|PD 60 CSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG 1ulk_A 117 CQSQ 121 120 |||. 124 2UVO:A|PD 120 CQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 39, 39, 40, 40, 80, 80, 81, 81, 121], [ 0, 38, 39, 40, 41, 81, 82, 83, 84, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['P', 'V', 'C', 'G', 'V', 'R', 'A', 'S', 'G', 'R', 'V', 'C', 'P', 'D', 'G', 'Y', 'C', 'C', 'S', 'Q', 'W', 'G', 'Y', 'C', 'G', 'T', 'T', 'E', 'E', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'S', 'Q', '-', 'C', '-', 'D', 'Y', 'N', 'R', 'C', 'G', 'K', 'E', 'F', 'G', 'G', 'K', 'E', 'C', 'H', 'D', 'E', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'W', 'C', 'G', 'N', 'S', 'D', 'G', 'H', 'C', 'G', 'E', 'G', 'C', 'Q', 'S', 'Q', '-', 'C', '-', 'S', 'Y', 'W', 'R', 'C', 'G', 'K', 'D', 'F', 'G', 'G', 'R', 'L', 'C', 'T', 'E', 'D', 'M', 'C', 'C', 'S', 'Q', 'Y', 'G', 'W', 'C', 'G', 'L', 'T', 'D', 'D', 'H', 'C', 'E', 'D', 'G', 'C', 'Q', 'S', 'Q'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.77) self.assertAlmostEqual(alignment.annotations["E-value"], 6.8e-24, places=25) self.assertAlmostEqual(alignment.annotations["Score"], 147.59) self.assertAlmostEqual(alignment.annotations["Identities"], 52) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.251) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 102.2) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[43:167], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSG", ) self.assertEqual( alignment[1], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~~c~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~gCq~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~cg~~~~~~~c~~g~CCs~~g~CG~~~~~Cg~gCq~~c~~~~Cg~~~~~~~c~~~~CCs~~G~CG~~~~~C~~~Cq~~c~~~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~C~~gCq~~ ", ) self.assertEqual(alignment.target.id, "1ulk_A") self.assertEqual( alignment.target.seq[1:121], "PVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQCDYNRCGKEFGGKECHDELCCSQYGWCGNSDGHCGEGCQSQCSYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDGCQSQ", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1ulk_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Lectin-C; chitin-binding protein, hevein domain, PL-C, sugar binding protein; 1.80A {Phytolacca americana} SCOP: g.3.1.1 g.3.1.1 g.3.1.1", ) self.assertEqual( alignment[0], "PVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQ-C-DYNRCGKEFGGKECHDELCCSQYGWCGNSDGHCGEGCQSQ-C-SYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDGCQSQ", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCSBGGGTTBCCGGGCEECTTSCEESSHHHHSTTCCBCTTTTBCBGGGTTBCCGGGCEECTTSBEECSHHHHSTTCCBCTTTTBCBGGGTTBCCSTTCEECTTSBEECSHHHHSTTCCBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CcCcCCCCCCCCCCCCeECCCCeeCCCccccCCCccccceeeeccccccCCCCCCccccCCCcccccCcccccCCcccccCcccccccCCCccCCCCcccccCceecCcccccCcccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 468888778999999999999999999999999998642345777654456788899999999999999999999997422467787555668999999999999999999999999984 ", ) self.assertEqual( str(alignment), """\ 1ulk_A 1 PVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQ-C-DYNRCGKEFGGKECHDELC 0 ..||..|.|..|....||||.||||...||||.|||..-|-....||...|||.|...|| 2UVO:A|PD 43 KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLC 1ulk_A 59 CSQYGWCGNSDGHCGEGCQSQ-C-SYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDG 60 |||.|.||.....||.||||.-|-....||||.|||.||...|||..|.||.....|..| 2UVO:A|PD 103 CSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAG 1ulk_A 117 CQSQ 121 120 |||. 124 2UVO:A|PD 163 CQSG 167 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 39, 39, 40, 40, 80, 80, 81, 81, 121], [ 43, 81, 82, 83, 84, 124, 125, 126, 127, 167]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['P', 'V', 'C', 'G', 'V', 'R', 'A', 'S', 'G', 'R', 'V', 'C', 'P', 'D', 'G', 'Y', 'C', 'C', 'S', 'Q', 'W', 'G', 'Y', 'C', 'G', 'T', 'T', 'E', 'E', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'S', 'Q', '-', 'C', '-', 'D', 'Y', 'N', 'R', 'C', 'G', 'K', 'E', 'F', 'G', 'G', 'K', 'E', 'C', 'H', 'D', 'E', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'W', 'C', 'G', 'N', 'S', 'D', 'G', 'H', 'C', 'G', 'E', 'G', 'C', 'Q', 'S', 'Q', '-', 'C', '-', 'S', 'Y', 'W', 'R', 'C', 'G', 'K', 'D', 'F', 'G', 'G', 'R', 'L', 'C', 'T', 'E', 'D', 'M', 'C', 'C', 'S', 'Q', 'Y', 'G', 'W', 'C', 'G', 'L', 'T', 'D', 'D', 'H', 'C', 'E', 'D', 'G', 'C', 'Q', 'S', 'Q'], ['K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.72) self.assertAlmostEqual(alignment.annotations["E-value"], 9.7e-23, places=24) self.assertAlmostEqual(alignment.annotations["Score"], 148.46) self.assertAlmostEqual(alignment.annotations["Identities"], 61) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.542) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 111.6) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[44:169], "RCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC", ) self.assertEqual( alignment[1], "RCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~~c~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~gCq~~~c ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~cg~~~~~~~c~~~~CCS~~g~Cg~~~~~Cg~gC~~~~c~~~~~cg~~~~~~~c~~~~CCs~~g~Cg~~~~~c~~~c~~~~~~~~~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~C~~gCq~~~c ", ) self.assertEqual(alignment.target.id, "2uvo_A") self.assertEqual( alignment.target.seq[1:126], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGAC", ) self.assertEqual(alignment.target.annotations["hmm_name"], "2uvo_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Agglutinin isolectin 1; carbohydrate-binding protein, hevein domain, chitin-binding, GERM agglutinin, chitin-binding protein; HET: NDG NAG GOL; 1.40A {Triticum aestivum} PDB: 1wgc_A* 2cwg_A* 2x3t_A* 4aml_A* 7wga_A 9wga_A 2wgc_A 1wgt_A 1k7t_A* 1k7v_A* 1k7u_A 2x52_A* 1t0w_A*", ) self.assertEqual( alignment[0], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGAC", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " BCBGGGTTBBCGGGCEECTTSBEEBSHHHHSTTCCBSSCSSCCBCBGGGTTBCCSTTCEECTTSBEEBSHHHHSTTCCBSSCSSCCBCBGGGTTBCCGGGCEECTTSBEEBSHHHHSTTCCBSSC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCcCCCCCCeeCCCCeECCCcccccCCccccccccccccCcccCCcccCCccccCCCceeCCCccccCCCcccccccccccccccccCCCCCCCcccCCCCccCCCcccccCCCcCCcc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 57776556789999999999999999999999999888888899998654567889999999999999999999999988888889999754456789999999999999999999999998755 ", ) self.assertEqual( str(alignment), """\ 2uvo_A 1 RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCC 0 |||.|.....|.||.|||||||||.|..|||.|||.|.|.....|||||||..|.||.|| 2UVO:A|PD 44 RCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCC 2uvo_A 61 SQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGC 60 ||.|.||.|.|.||.|||.|.|..|..||..|||..|.||.|||.||.||.|...||.|| 2UVO:A|PD 104 SQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGC 2uvo_A 121 QSGAC 126 120 |||.| 125 2UVO:A|PD 164 QSGGC 169 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 126], [ 44, 169]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C'], ['R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G', 'G', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.66) self.assertAlmostEqual(alignment.annotations["E-value"], 2.4e-21, places=22) self.assertAlmostEqual(alignment.annotations["Score"], 140.12) self.assertAlmostEqual(alignment.annotations["Identities"], 41) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.182) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[45:170], "CGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCD", ) self.assertEqual( alignment[1], "CGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCD", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " Cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~~c~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~gCq~~~c~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~g~~~~~~~c~~~~CCs~~g~Cg~~~~~c~~~C~~~~c~~~~~cg~~~~~c~~~~CCs~~G~CG~~~~~C~~~C~~~~~~~~~~Cg~~~~~c~~~~Ccs~~G~CGt~~~~C~~~cq~~~c~ ", ) self.assertEqual(alignment.target.id, "2wga") self.assertEqual( alignment.target.seq[2:123], "XGCXGXXMYCSTNNCCXXWESCGSGGYXCGEGCNLGACQXGXPCXXPGSVCTNLHCCARGGHCGMGSGYCGXGCXGGACXADIXCGXGXXXCPTDSCCGGWGXCGNGXEFCGXGCXVGGCA", ) self.assertEqual(alignment.target.annotations["hmm_name"], "2wga") self.assertEqual( alignment.target.annotations["hmm_description"], "; lectin (agglutinin); NMR {}", ) self.assertEqual( alignment[0], "XGCXGXXMYCSTNNCCXXWESCGSGGYXCGEGCNLGACQXGXPCXX--PGSVCTNLHCCARGGHCGMGSGYCGXGCXGGACXADIXCGXG--XXXCPTDSCCGGWGXCGNGXEFCGXGCXVGGCA", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " SGGGSSCCCCSTTCEECTTSCEECSTTTTSTTCCSSSCSSCCCSSSSSCCCSTTCEECTTSCEESSHHHHSSCCSSSSCSSCCCCTTSSSCCSTTCBCCSSSCCBCSHHHHSTTCCSSSCS ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCCCcccccCCCCceECCcceECCCCccccCccccCcccccceeccCCCcCCCCcccCCCceeCCCCcccCCCccccccccccccCcccccCCCCCccCCCCCccCccccccCCccccccc ", ) self.assertEqual( str(alignment), """\ 2wga 2 XGCXGXXMYCSTNNCCXXWESCGSGGYXCGEGCNLGACQXGXPCXX--PGSVCTNLHCCA 0 .|.......|..|.||.....||.|...||.||..|.|.....|..--.|..|.|..||. 2UVO:A|PD 45 CGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCS 2wga 60 RGGHCGMGSGYCGXGCXGGACXADIXCGXG--XXXCPTDSCCGGWGXCGNGXEFCGXGCX 60 ..|.||.||..||.||..|||..|..||..--...|....||..||.||.|...||.||. 2UVO:A|PD 105 QWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQ 2wga 118 VGGCA 123 120 .|||. 125 2UVO:A|PD 165 SGGCD 170 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 48, 48, 90, 90, 123], [ 45, 91, 93, 135, 137, 170]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['X', 'G', 'C', 'X', 'G', 'X', 'X', 'M', 'Y', 'C', 'S', 'T', 'N', 'N', 'C', 'C', 'X', 'X', 'W', 'E', 'S', 'C', 'G', 'S', 'G', 'G', 'Y', 'X', 'C', 'G', 'E', 'G', 'C', 'N', 'L', 'G', 'A', 'C', 'Q', 'X', 'G', 'X', 'P', 'C', 'X', 'X', '-', '-', 'P', 'G', 'S', 'V', 'C', 'T', 'N', 'L', 'H', 'C', 'C', 'A', 'R', 'G', 'G', 'H', 'C', 'G', 'M', 'G', 'S', 'G', 'Y', 'C', 'G', 'X', 'G', 'C', 'X', 'G', 'G', 'A', 'C', 'X', 'A', 'D', 'I', 'X', 'C', 'G', 'X', 'G', '-', '-', 'X', 'X', 'X', 'C', 'P', 'T', 'D', 'S', 'C', 'C', 'G', 'G', 'W', 'G', 'X', 'C', 'G', 'N', 'G', 'X', 'E', 'F', 'C', 'G', 'X', 'G', 'C', 'X', 'V', 'G', 'G', 'C', 'A'], ['C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G', 'G', 'C', 'D']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.31) self.assertAlmostEqual(alignment.annotations["E-value"], 1.2e-16, places=17) self.assertAlmostEqual(alignment.annotations["Score"], 102.02) self.assertAlmostEqual(alignment.annotations["Identities"], 47) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.275) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 66.8) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[43:123], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQS", ) self.assertEqual( alignment[1], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQS", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~cg~~~~~~~C~~g~CCs~~G~Cg~~~~~c~~~c~~~~~~g~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~C~~~Cqs ", ) self.assertEqual(alignment.target.id, "1uha_A") self.assertEqual( alignment.target.seq[1:79], "PECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQCDYWRCGRDFGGRLCEEDMCCSKYGWCGYSDDHCEDGCQS", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1uha_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Lectin-D2; chitin-binding domain, sugar binding protein; 1.50A {Phytolacca americana} SCOP: g.3.1.1 g.3.1.1 PDB: 1ulm_A* 1uln_A", ) self.assertEqual( alignment[0], "PECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQ--CDYWRCGRDFGGRLCEEDMCCSKYGWCGYSDDHCEDGCQS", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCSBGGGTTBCCGGGCEECTTSCEESSHHHHSTTCCBCTTTTBCBGGGTTBCCSTTCEECTTSBEECSHHHHSTTCCB ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCcCCCCCccCCCccccCccccccCCccccccccccccccceecCCCCCccCCCccccCCcccccccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 467776667789999999999999999999999998642356788765567788999999999999999999999986 ", ) self.assertEqual( str(alignment), """\ 1uha_A 1 PECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQ--CDYWRCGRDFGGRLCEEDMC 0 ..||..|.|..|.|..||||.||||....|||.|||..--.....||...||.||....| 2UVO:A|PD 43 KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLC 1uha_A 59 CSKYGWCGYSDDHCEDGCQS 79 60 ||..|.||.....|..|||| 80 2UVO:A|PD 103 CSQWGFCGLGSEFCGGGCQS 123 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 39, 39, 79], [ 43, 81, 83, 123]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['P', 'E', 'C', 'G', 'E', 'R', 'A', 'S', 'G', 'K', 'R', 'C', 'P', 'N', 'G', 'K', 'C', 'C', 'S', 'Q', 'W', 'G', 'Y', 'C', 'G', 'T', 'T', 'D', 'N', 'Y', 'C', 'G', 'Q', 'G', 'C', 'Q', 'S', 'Q', '-', '-', 'C', 'D', 'Y', 'W', 'R', 'C', 'G', 'R', 'D', 'F', 'G', 'G', 'R', 'L', 'C', 'E', 'E', 'D', 'M', 'C', 'C', 'S', 'K', 'Y', 'G', 'W', 'C', 'G', 'Y', 'S', 'D', 'D', 'H', 'C', 'E', 'D', 'G', 'C', 'Q', 'S'], ['K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.26) self.assertAlmostEqual(alignment.annotations["E-value"], 3.7e-16, places=17) self.assertAlmostEqual(alignment.annotations["Score"], 101.24) self.assertAlmostEqual(alignment.annotations["Identities"], 47) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.259) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 71.9) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:82], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGP", ) self.assertEqual( alignment[1], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACW----TSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAG-CQGGP", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~c~~~~~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~~cg~~~~~~~C~~~~CCS~~G~CG~~~~~C~~~Cq~~c~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~~Cq~~~ ", ) self.assertEqual(alignment.target.id, "1en2_A") self.assertEqual( alignment.target.seq[0:86], "ERCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYRC", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1en2_A") self.assertEqual( alignment.target.annotations["hmm_description"], "UDA, agglutinin isolectin I/agglutinin isolectin V/ AG isolectin VI; hevein domain, superantigen, saccharide binding binding protein; HET: NAG; 1.40A {Urtica dioica} SCOP: g.3.1.1 g.3.1.1 PDB: 1eis_A* 1enm_A* 1ehd_A 1ehh_A* 1iqb_A", ) self.assertEqual( alignment[0], "ERCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENK-CWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYRC", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CBCTTTTTSCCCGGGCEEETTSBEESSHHHHSTTEEESCGGGCCTTCBCSGGGTCCCCCTTCEEETTSBEESSHHHHSGGGEEECC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCCCCCCCCccCCCCcccCCCceecccccccCCCCcCCCcccccCCcccCCcccccccCCCCeECCCceECCCccccCCCCcccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], "6899999889999999999999999999999999997643 478899865567889999999999999999999986 98753 ", ) self.assertEqual( str(alignment), """\ 1en2_A 0 ERCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENK-CWSGERSDHRCGAAVGNPPCG 0 ||||.||....||...|||..|.||....|||..|.|.-||----...|||...|...|. 2UVO:A|PD 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACW----TSKRCGSQAGGATCT 1en2_A 59 QDRCCSVHGWCGGGNDYCSGGNCQYRC 86 60 ...|||..|.||.|..||..|-||... 87 2UVO:A|PD 56 NNQCCSQYGYCGFGAEYCGAG-CQGGP 82 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 38, 38, 40, 44, 80, 81, 86], [ 0, 38, 39, 41, 41, 77, 77, 82]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'R', 'C', 'G', 'S', 'Q', 'G', 'G', 'G', 'S', 'T', 'C', 'P', 'G', 'L', 'R', 'C', 'C', 'S', 'I', 'W', 'G', 'W', 'C', 'G', 'D', 'S', 'E', 'P', 'Y', 'C', 'G', 'R', 'T', 'C', 'E', 'N', 'K', '-', 'C', 'W', 'S', 'G', 'E', 'R', 'S', 'D', 'H', 'R', 'C', 'G', 'A', 'A', 'V', 'G', 'N', 'P', 'P', 'C', 'G', 'Q', 'D', 'R', 'C', 'C', 'S', 'V', 'H', 'G', 'W', 'C', 'G', 'G', 'G', 'N', 'D', 'Y', 'C', 'S', 'G', 'G', 'N', 'C', 'Q', 'Y', 'R', 'C'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', '-', '-', '-', '-', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', '-', 'C', 'Q', 'G', 'G', 'P']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.22) self.assertAlmostEqual(alignment.annotations["E-value"], 7.4e-16, places=17) self.assertAlmostEqual(alignment.annotations["Score"], 99.76) self.assertAlmostEqual(alignment.annotations["Identities"], 47) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.232) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 67.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[44:124], "RCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG", ) self.assertEqual( alignment[1], "RCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCR----ADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG-CQSG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~cg~~~~~~~C~~~~CCS~~G~CG~~~~~C~~~Cq~~c~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "1en2_A") self.assertEqual( alignment.target.seq[1:85], "RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYR", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1en2_A") self.assertEqual( alignment.target.annotations["hmm_description"], "UDA, agglutinin isolectin I/agglutinin isolectin V/ AG isolectin VI; hevein domain, superantigen, saccharide binding binding protein; HET: NAG; 1.40A {Urtica dioica} SCOP: g.3.1.1 g.3.1.1 PDB: 1eis_A* 1enm_A* 1ehd_A 1ehh_A* 1iqb_A", ) self.assertEqual( alignment[0], "RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENK-CWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYR", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " BCTTTTTSCCCGGGCEEETTSBEESSHHHHSTTEEESCGGGCCTTCBCSGGGTCCCCCTTCEEETTSBEESSHHHHSGGGEEEC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCccCCCCcccCCCceecccccccCCCCcCCCcccccCCcccCCcccccccCCCCeECCCceECCCccccCCCCcccC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 577766667899999999999999999999999987543 478888765456788999999999999999999997 9974 ", ) self.assertEqual( str(alignment), """\ 1en2_A 1 RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENK-CWSGERSDHRCGAAVGNPPCGQ 0 |||||.||.||....|||..|.||....|||..|...-|.----.|..||...|...|.. 2UVO:A|PD 44 RCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCR----ADIKCGSQAGGKLCPN 1en2_A 60 DRCCSVHGWCGGGNDYCSGGNCQYR 85 60 ..|||..|.||.|...|.||-||.. 85 2UVO:A|PD 100 NLCCSQWGFCGLGSEFCGGG-CQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 38, 38, 40, 44, 80, 81, 85], [ 44, 81, 82, 84, 84, 120, 120, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'C', 'G', 'S', 'Q', 'G', 'G', 'G', 'S', 'T', 'C', 'P', 'G', 'L', 'R', 'C', 'C', 'S', 'I', 'W', 'G', 'W', 'C', 'G', 'D', 'S', 'E', 'P', 'Y', 'C', 'G', 'R', 'T', 'C', 'E', 'N', 'K', '-', 'C', 'W', 'S', 'G', 'E', 'R', 'S', 'D', 'H', 'R', 'C', 'G', 'A', 'A', 'V', 'G', 'N', 'P', 'P', 'C', 'G', 'Q', 'D', 'R', 'C', 'C', 'S', 'V', 'H', 'G', 'W', 'C', 'G', 'G', 'G', 'N', 'D', 'Y', 'C', 'S', 'G', 'G', 'N', 'C', 'Q', 'Y', 'R'], ['R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', '-', '-', '-', '-', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', '-', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.21) self.assertAlmostEqual(alignment.annotations["E-value"], 9.6e-16, places=17) self.assertAlmostEqual(alignment.annotations["Score"], 97.65) self.assertAlmostEqual(alignment.annotations["Identities"], 54) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.333) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 65.9) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[87:167], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSG", ) self.assertEqual( alignment[1], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~~c~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~gCq~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~cg~~~~~~~C~~g~CCs~~G~Cg~~~~~c~~~c~~~~~~g~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~C~~~Cqs~ ", ) self.assertEqual(alignment.target.id, "1uha_A") self.assertEqual( alignment.target.seq[2:80], "ECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQCDYWRCGRDFGGRLCEEDMCCSKYGWCGYSDDHCEDGCQSQ", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1uha_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Lectin-D2; chitin-binding domain, sugar binding protein; 1.50A {Phytolacca americana} SCOP: g.3.1.1 g.3.1.1 PDB: 1ulm_A* 1uln_A", ) self.assertEqual( alignment[0], "ECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQ-C-DYWRCGRDFGGRLCEEDMCCSKYGWCGYSDDHCEDGCQSQ", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSBGGGTTBCCGGGCEECTTSCEESSHHHHSTTCCBCTTTTBCBGGGTTBCCSTTCEECTTSBEECSHHHHSTTCCBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCcCCCCCccCCCccccCccccccCCccccccccccccccceecCCCCCccCCCccccCCccccccccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 466654457789999999999999999999999997423467887655678899999999999999999999999974 ", ) self.assertEqual( str(alignment), """\ 1uha_A 2 ECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQ-C-DYWRCGRDFGGRLCEEDMCC 0 .||..|.||.|||..||||||.||.....||.||||.-|-....||.|.|||.|....|| 2UVO:A|PD 87 KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCC 1uha_A 60 SKYGWCGYSDDHCEDGCQSQ 80 60 ||.|.||.....|..||||. 80 2UVO:A|PD 147 SKWGSCGIGPGYCGAGCQSG 167 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 39, 39, 40, 40, 80], [ 87, 124, 125, 126, 127, 167]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'C', 'G', 'E', 'R', 'A', 'S', 'G', 'K', 'R', 'C', 'P', 'N', 'G', 'K', 'C', 'C', 'S', 'Q', 'W', 'G', 'Y', 'C', 'G', 'T', 'T', 'D', 'N', 'Y', 'C', 'G', 'Q', 'G', 'C', 'Q', 'S', 'Q', '-', 'C', '-', 'D', 'Y', 'W', 'R', 'C', 'G', 'R', 'D', 'F', 'G', 'G', 'R', 'L', 'C', 'E', 'E', 'D', 'M', 'C', 'C', 'S', 'K', 'Y', 'G', 'W', 'C', 'G', 'Y', 'S', 'D', 'D', 'H', 'C', 'E', 'D', 'G', 'C', 'Q', 'S', 'Q'], ['K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.79) self.assertAlmostEqual(alignment.annotations["E-value"], 7.7e-09, places=10) self.assertAlmostEqual(alignment.annotations["Score"], 56.76) self.assertAlmostEqual(alignment.annotations["Identities"], 68) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.600) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 30.2) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[87:124], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG" ) self.assertEqual(alignment[1], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGG--GCQSG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~CG~~~~~~~C~~~~CCS~~G~CG~t~~~C~~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "1wkx_A") self.assertEqual( alignment.target.seq[1:40], "QCGRQAGGKLCPDNLCCSQWGWCGSTDEYCSPDHNCQSN" ) self.assertEqual(alignment.target.annotations["hmm_name"], "1wkx_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Hevein isoform 2; allergen, lectin, agglutinin-toxin motif; 1.70A {Hevea brasiliensis} PDB: 1hev_A 1q9b_A* 4wp4_A", ) self.assertEqual(alignment[0], "QCGRQAGGKLCPDNLCCSQWGWCGSTDEYCSPDHNCQSN") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSBGGGTTBCCSTTCEECTTSCEESSHHHHCGGGTCCBS ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCcCCCcccCCCCeEeecCcccCCcccccCCCCccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 35554445678899999999999999999986 79874 ", ) self.assertEqual( str(alignment), """\ 1wkx_A 1 QCGRQAGGKLCPDNLCCSQWGWCGSTDEYCSPDHNCQSN 40 0 .||.||||||||.||||||||.||...|.|..--.|||. 39 2UVO:A|PD 87 KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGG--GCQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 33, 35, 40], [ 87, 119, 119, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['Q', 'C', 'G', 'R', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'D', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'W', 'C', 'G', 'S', 'T', 'D', 'E', 'Y', 'C', 'S', 'P', 'D', 'H', 'N', 'C', 'Q', 'S', 'N'], ['K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', '-', '-', 'G', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.67) self.assertAlmostEqual(alignment.annotations["E-value"], 1.9e-08, places=9) self.assertAlmostEqual(alignment.annotations["Score"], 54.61) self.assertAlmostEqual(alignment.annotations["Identities"], 46) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.182) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 32.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:38], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNG" ) self.assertEqual(alignment[1], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGK-GCQNG") self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~~CG~~~~~~C~~~~CCS~~G~CG~t~~~C~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "1p9g_A") self.assertEqual( alignment.target.seq[0:38], "ETCASRCPRPCNAGLCCSIYGYCGSGAAYCGAGNCRCQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "1p9g_A") self.assertEqual( alignment.target.annotations["hmm_description"], "EAFP 2; antifungal peptide, atomic resolution, antifungal protein; HET: PCA; 0.84A {Eucommia ulmoides} SCOP: g.3.1.1 PDB: 1p9z_A*", ) self.assertEqual(alignment[0], "ETCAS-RCPRPCNAGLCCSIYGYCGSGAAYCGAGNCRCQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CCGGGGTTCCSCTTCEEETTSCEECSHHHHSTTTEEEC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCcCCcCCcccCCCCeECccceeCCCccccCCCccccC ", ) self.assertEqual( alignment.column_annotations["Confidence"], "68995677899999999999999999999998 49864 ", ) self.assertEqual( str(alignment), """\ 1p9g_A 0 ETCAS-RCPRPCNAGLCCSIYGYCGSGAAYCGAGNCRCQ 38 0 |.|..-.....|...||||.|||||.|..|||.-.|... 39 2UVO:A|PD 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGK-GCQNG 38 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 5, 5, 32, 33, 38], [ 0, 5, 6, 33, 33, 38]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'T', 'C', 'A', 'S', '-', 'R', 'C', 'P', 'R', 'P', 'C', 'N', 'A', 'G', 'L', 'C', 'C', 'S', 'I', 'Y', 'G', 'Y', 'C', 'G', 'S', 'G', 'A', 'A', 'Y', 'C', 'G', 'A', 'G', 'N', 'C', 'R', 'C', 'Q'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', '-', 'G', 'C', 'Q', 'N', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.66) self.assertAlmostEqual(alignment.annotations["E-value"], 1.9e-08, places=9) self.assertAlmostEqual(alignment.annotations["Score"], 54.54) self.assertAlmostEqual(alignment.annotations["Identities"], 42) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.206) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 29.2) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[87:124], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG" ) self.assertEqual(alignment[1], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG-CQSG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~CG~~~~~~C~~~~CCS~~G~CG~t~~~C~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "1p9g_A") self.assertEqual( alignment.target.seq[1:38], "TCASRCPRPCNAGLCCSIYGYCGSGAAYCGAGNCRCQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "1p9g_A") self.assertEqual( alignment.target.annotations["hmm_description"], "EAFP 2; antifungal peptide, atomic resolution, antifungal protein; HET: PCA; 0.84A {Eucommia ulmoides} SCOP: g.3.1.1 PDB: 1p9z_A*", ) self.assertEqual(alignment[0], "TCAS-RCPRPCNAGLCCSIYGYCGSGAAYCGAGNCRCQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CGGGGTTCCSCTTCEEETTSCEECSHHHHSTTTEEEC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CcCCcCCcccCCCCeECccceeCCCccccCCCccccC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 35533356788999999999999999999984 9874 ", ) self.assertEqual( str(alignment), """\ 1p9g_A 1 TCAS-RCPRPCNAGLCCSIYGYCGSGAAYCGAGNCRCQ 38 0 .|.|-.....|...||||..|.||.|...||.|-|... 38 2UVO:A|PD 87 KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG-CQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 5, 5, 33, 34, 38], [ 87, 91, 92, 120, 120, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'C', 'A', 'S', '-', 'R', 'C', 'P', 'R', 'P', 'C', 'N', 'A', 'G', 'L', 'C', 'C', 'S', 'I', 'Y', 'G', 'Y', 'C', 'G', 'S', 'G', 'A', 'A', 'Y', 'C', 'G', 'A', 'G', 'N', 'C', 'R', 'C', 'Q'], ['K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', '-', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.65) self.assertAlmostEqual(alignment.annotations["E-value"], 2e-08, places=9) self.assertAlmostEqual(alignment.annotations["Score"], 54.99) self.assertAlmostEqual(alignment.annotations["Identities"], 50) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.302) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 34.5) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:38], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNG" ) self.assertEqual(alignment[1], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGK--GCQNG") self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~~CG~~~~~~~C~~~~CCS~~G~CG~t~~~C~~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "1wkx_A") self.assertEqual( alignment.target.seq[0:40], "EQCGRQAGGKLCPDNLCCSQWGWCGSTDEYCSPDHNCQSN" ) self.assertEqual(alignment.target.annotations["hmm_name"], "1wkx_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Hevein isoform 2; allergen, lectin, agglutinin-toxin motif; 1.70A {Hevea brasiliensis} PDB: 1hev_A 1q9b_A* 4wp4_A", ) self.assertEqual(alignment[0], "EQCGRQAGGKLCPDNLCCSQWGWCGSTDEYCSPDHNCQSN") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CCSBGGGTTBCCSTTCEECTTSCEESSHHHHCGGGTCCBS ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCCCCcCCCcccCCCCeEeecCcccCCcccccCCCCccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], "579999888899999999999999999999996 79864 ", ) self.assertEqual( str(alignment), """\ 1wkx_A 0 EQCGRQAGGKLCPDNLCCSQWGWCGSTDEYCSPDHNCQSN 40 0 |.||.|.....||.||||||.|.||....||..--.||.. 40 2UVO:A|PD 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGK--GCQNG 38 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 33, 35, 40], [ 0, 33, 33, 38]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'Q', 'C', 'G', 'R', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'D', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'W', 'C', 'G', 'S', 'T', 'D', 'E', 'Y', 'C', 'S', 'P', 'D', 'H', 'N', 'C', 'Q', 'S', 'N'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', '-', '-', 'G', 'C', 'Q', 'N', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.62) self.assertAlmostEqual(alignment.annotations["E-value"], 2.4e-08, places=9) self.assertAlmostEqual(alignment.annotations["Score"], 55.16) self.assertAlmostEqual(alignment.annotations["Identities"], 51) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.325) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 33.8) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:38], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNG" ) self.assertEqual(alignment[1], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~CG~~~~~~~C~~~~CCs~~G~CG~t~~~C~~gCq~~ ", ) self.assertEqual(alignment.target.id, "4mpi_A") self.assertEqual( alignment.target.seq[3:40], "QCGRQAGGALCPGGLCCSQYGWCANTPEYCGSGCQSQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "4mpi_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Class I chitinase; hevein-like domain, chitin oligomers, sugar binding protein; HET: MES; 1.60A {Hevea brasiliensis subsp}", ) self.assertEqual(alignment[0], "QCGRQAGGALCPGGLCCSQYGWCANTPEYCGSGCQSQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " BCBGGGTTBCCGGGCEECTTSBEECSHHHHSTTCCBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ccCCcCCCcccCCCCcCcccceecCCccccccccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 6888887789999999999999999999999999864 ", ) self.assertEqual( str(alignment), """\ 4mpi_A 3 QCGRQAGGALCPGGLCCSQYGWCANTPEYCGSGCQSQ 40 0 .||.|.....||..|||||||.|.....|||.|||.. 37 2UVO:A|PD 1 RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNG 38 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 3, 40], [ 1, 38]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['Q', 'C', 'G', 'R', 'Q', 'A', 'G', 'G', 'A', 'L', 'C', 'P', 'G', 'G', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'W', 'C', 'A', 'N', 'T', 'P', 'E', 'Y', 'C', 'G', 'S', 'G', 'C', 'Q', 'S', 'Q'], ['R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.59) self.assertAlmostEqual(alignment.annotations["E-value"], 3e-08, places=9) self.assertAlmostEqual(alignment.annotations["Score"], 54.44) self.assertAlmostEqual(alignment.annotations["Identities"], 59) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.493) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 30.2) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[87:124], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG" ) self.assertEqual(alignment[1], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG-CQSG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~CG~~~~~~~C~~~~CCS~~G~CG~t~~~C~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "2lb7_A") self.assertEqual( alignment.target.seq[2:40], "RCGDQARGAKCPNCLCCGKYGFCGSGDAYCGAGSCQSQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "2lb7_A") self.assertEqual( alignment.target.annotations["hmm_description"], "WAMP-1A, antimicrobial peptide 1A; antimicrobial protein; NMR {Triticum kiharae}", ) self.assertEqual(alignment[0], "RCGDQARGAKCPNCLCCGKYGFCGSGDAYCGAGSCQSQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " ECBGGGTTBCCCTTCEEETTTEEECSHHHHSTTSEEEC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCcCCCCCcccCCCCcCCcceeecCCccccCCCCccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 455544456788999999999999999999986 8864 ", ) self.assertEqual( str(alignment), """\ 2lb7_A 2 RCGDQARGAKCPNCLCCGKYGFCGSGDAYCGAGSCQSQ 40 0 .||.||.|..|||.|||...||||.|...||.|-|||. 38 2UVO:A|PD 87 KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG-CQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 35, 36, 40], [ 87, 120, 120, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'C', 'G', 'D', 'Q', 'A', 'R', 'G', 'A', 'K', 'C', 'P', 'N', 'C', 'L', 'C', 'C', 'G', 'K', 'Y', 'G', 'F', 'C', 'G', 'S', 'G', 'D', 'A', 'Y', 'C', 'G', 'A', 'G', 'S', 'C', 'Q', 'S', 'Q'], ['K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', '-', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.57) self.assertAlmostEqual(alignment.annotations["E-value"], 3.3e-08, places=9) self.assertAlmostEqual(alignment.annotations["Score"], 54.59) self.assertAlmostEqual(alignment.annotations["Identities"], 61) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.420) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 31.3) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[86:124], "IKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG" ) self.assertEqual(alignment[1], "IKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~CG~~~~~~~C~~~~CCs~~G~CG~t~~~C~~gCq~~ ", ) self.assertEqual(alignment.target.id, "4mpi_A") self.assertEqual( alignment.target.seq[2:40], "EQCGRQAGGALCPGGLCCSQYGWCANTPEYCGSGCQSQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "4mpi_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Class I chitinase; hevein-like domain, chitin oligomers, sugar binding protein; HET: MES; 1.60A {Hevea brasiliensis subsp}", ) self.assertEqual(alignment[0], "EQCGRQAGGALCPGGLCCSQYGWCANTPEYCGSGCQSQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CBCBGGGTTBCCGGGCEECTTSBEECSHHHHSTTCCBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cccCCcCCCcccCCCCcCcccceecCCccccccccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 45665544567889999999999999999999999873 ", ) self.assertEqual( str(alignment), """\ 4mpi_A 2 EQCGRQAGGALCPGGLCCSQYGWCANTPEYCGSGCQSQ 40 0 ..||.||||.|||..|||||.|.|....|.||.||||. 38 2UVO:A|PD 86 IKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 40], [ 86, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'Q', 'C', 'G', 'R', 'Q', 'A', 'G', 'G', 'A', 'L', 'C', 'P', 'G', 'G', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'W', 'C', 'A', 'N', 'T', 'P', 'E', 'Y', 'C', 'G', 'S', 'G', 'C', 'Q', 'S', 'Q'], ['I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.46) self.assertAlmostEqual(alignment.annotations["E-value"], 6.6e-08, places=9) self.assertAlmostEqual(alignment.annotations["Score"], 52.98) self.assertAlmostEqual(alignment.annotations["Identities"], 55) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.488) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 34.0) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:38], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNG" ) self.assertEqual(alignment[1], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKG-CQNG") self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~CG~~~~~~~C~~~~CCS~~G~CG~t~~~C~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "2lb7_A") self.assertEqual( alignment.target.seq[1:40], "QRCGDQARGAKCPNCLCCGKYGFCGSGDAYCGAGSCQSQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "2lb7_A") self.assertEqual( alignment.target.annotations["hmm_description"], "WAMP-1A, antimicrobial peptide 1A; antimicrobial protein; NMR {Triticum kiharae}", ) self.assertEqual(alignment[0], "QRCGDQARGAKCPNCLCCGKYGFCGSGDAYCGAGSCQSQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " EECBGGGTTBCCCTTCEEETTTEEECSHHHHSTTSEEEC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCcCCCCCcccCCCCcCCcceeecCCccccCCCCccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 4789998778999999999999999999999986 8864 ", ) self.assertEqual( str(alignment), """\ 2lb7_A 1 QRCGDQARGAKCPNCLCCGKYGFCGSGDAYCGAGSCQSQ 40 0 .|||.|.....|||.|||..||.||.|..|||.|-||.. 39 2UVO:A|PD 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKG-CQNG 38 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 35, 36, 40], [ 0, 34, 34, 38]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['Q', 'R', 'C', 'G', 'D', 'Q', 'A', 'R', 'G', 'A', 'K', 'C', 'P', 'N', 'C', 'L', 'C', 'C', 'G', 'K', 'Y', 'G', 'F', 'C', 'G', 'S', 'G', 'D', 'A', 'Y', 'C', 'G', 'A', 'G', 'S', 'C', 'Q', 'S', 'Q'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', '-', 'C', 'Q', 'N', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.25) self.assertAlmostEqual(alignment.annotations["E-value"], 2.2e-07, places=8) self.assertAlmostEqual(alignment.annotations["Score"], 48.31) self.assertAlmostEqual(alignment.annotations["Identities"], 50) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.296) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 27.1) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[41:75], "TSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCG" ) self.assertEqual(alignment[1], "TSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~CG~~~g~C~~g~CCS~~G~CG~~~~~C~ ", ) self.assertEqual(alignment.target.id, "2kus_A") self.assertEqual(alignment.target.seq[2:34], "PNGQCGPGWGGCRGGLCCSQYGYCGSGPKYCA") self.assertEqual(alignment.target.annotations["hmm_name"], "2kus_A") self.assertEqual( alignment.target.annotations["hmm_description"], "SM-AMP-1.1A; plant antimicrobial peptide, chitin-binding peptide, antimic protein; NMR {Stellaria media}", ) self.assertEqual(alignment[0], "PNGQCGPGWG--GCRGGLCCSQYGYCGSGPKYCA") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " TTCBCBTTTBCCCTTCEECTTSBEECSHHHHC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCcccCCCCCcCCCCcEECCCceecCChhhhC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 45678875436899999999999999999986 ", ) self.assertEqual( str(alignment), """\ 2kus_A 2 PNGQCGPGWG--GCRGGLCCSQYGYCGSGPKYCA 34 0 ....||...|--.|....|||||||||.|..||. 34 2UVO:A|PD 41 TSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCG 75 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 12, 12, 34], [41, 51, 53, 75]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['P', 'N', 'G', 'Q', 'C', 'G', 'P', 'G', 'W', 'G', '-', '-', 'G', 'C', 'R', 'G', 'G', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'S', 'G', 'P', 'K', 'Y', 'C', 'A'], ['T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.13) self.assertAlmostEqual(alignment.annotations["E-value"], 4.2e-07, places=8) self.assertAlmostEqual(alignment.annotations["Score"], 47.19) self.assertAlmostEqual(alignment.annotations["Identities"], 44) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.207) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 26.5) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[84:118], "ADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCG" ) self.assertEqual(alignment[1], "ADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~CG~~~g~C~~g~CCS~~G~CG~~~~~C~ ", ) self.assertEqual(alignment.target.id, "2kus_A") self.assertEqual(alignment.target.seq[2:34], "PNGQCGPGWGGCRGGLCCSQYGYCGSGPKYCA") self.assertEqual(alignment.target.annotations["hmm_name"], "2kus_A") self.assertEqual( alignment.target.annotations["hmm_description"], "SM-AMP-1.1A; plant antimicrobial peptide, chitin-binding peptide, antimic protein; NMR {Stellaria media}", ) self.assertEqual(alignment[0], "PNGQCGPGWG--GCRGGLCCSQYGYCGSGPKYCA") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " TTCBCBTTTBCCCTTCEECTTSBEECSHHHHC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCcccCCCCCcCCCCcEECCCceecCChhhhC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 45677775436889999999999999999986 ", ) self.assertEqual( str(alignment), """\ 2kus_A 2 PNGQCGPGWG--GCRGGLCCSQYGYCGSGPKYCA 34 0 ....||...|--.|...|||||.|.||.|...|. 34 2UVO:A|PD 84 ADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCG 118 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 12, 12, 34], [ 84, 94, 96, 118]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['P', 'N', 'G', 'Q', 'C', 'G', 'P', 'G', 'W', 'G', '-', '-', 'G', 'C', 'R', 'G', 'G', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'S', 'G', 'P', 'K', 'Y', 'C', 'A'], ['A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.04) self.assertAlmostEqual(alignment.annotations["E-value"], 6.8e-07, places=8) self.assertAlmostEqual(alignment.annotations["Score"], 44.77) self.assertAlmostEqual(alignment.annotations["Identities"], 48) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.444) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 22.0) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual(alignment.query.seq[94:119], "GKLCPNNLCCSQWGFCGLGSEFCGG") self.assertEqual(alignment[1], "GKLCPNNLCCSQWGFCGLGSEFCGG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~c~~~~CCS~~G~CG~~~~~C~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~C~~~~CCS~~G~CG~t~~~C~~", ) self.assertEqual(alignment.target.id, "1mmc_A") self.assertEqual(alignment.target.seq[5:30], "RGRCPSGMCCSQFGYCGKGPKYCGR") self.assertEqual(alignment.target.annotations["hmm_name"], "1mmc_A") self.assertEqual( alignment.target.annotations["hmm_description"], "AC-AMP2, antimicrobial peptide 2; antifungal antimicrobial, chitin-binding; NMR {Amaranthus caudatus} SCOP: g.3.1.2 PDB: 1zuv_A 1zwu_A* 1znt_A*", ) self.assertEqual(alignment[0], "RGRCPSGMCCSQFGYCGKGPKYCGR") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " SSCCSTTCEECTTSCEESSHHHHCC", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCCCCCCCcccccceeCCchHhhCc", ) self.assertEqual( alignment.column_annotations["Confidence"], " 3468899999999999999999963", ) self.assertEqual( str(alignment), """\ 1mmc_A 5 RGRCPSGMCCSQFGYCGKGPKYCGR 30 0 ...||...||||.|.||.|...||. 25 2UVO:A|PD 94 GKLCPNNLCCSQWGFCGLGSEFCGG 119 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 5, 30], [ 94, 119]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'G', 'R', 'C', 'P', 'S', 'G', 'M', 'C', 'C', 'S', 'Q', 'F', 'G', 'Y', 'C', 'G', 'K', 'G', 'P', 'K', 'Y', 'C', 'G', 'R'], ['G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 96.99) self.assertAlmostEqual(alignment.annotations["E-value"], 8.4e-07, places=8) self.assertAlmostEqual(alignment.annotations["Score"], 44.41) self.assertAlmostEqual(alignment.annotations["Identities"], 52) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.425) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 23.6) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual(alignment.query.seq[6:33], "GSNMECPNNLCCSQYGYCGMGGDYCGK") self.assertEqual(alignment[1], "GSNMECPNNLCCSQYGYCGMGGDYCGK") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~c~~~~CCs~~g~CG~~~~~c~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~C~~~~CCS~~G~CG~t~~~C~~", ) self.assertEqual(alignment.target.id, "1mmc_A") self.assertEqual(alignment.target.seq[3:30], "CVRGRCPSGMCCSQFGYCGKGPKYCGR") self.assertEqual(alignment.target.annotations["hmm_name"], "1mmc_A") self.assertEqual( alignment.target.annotations["hmm_description"], "AC-AMP2, antimicrobial peptide 2; antifungal antimicrobial, chitin-binding; NMR {Amaranthus caudatus} SCOP: g.3.1.2 PDB: 1zuv_A 1zwu_A* 1znt_A*", ) self.assertEqual(alignment[0], "CVRGRCPSGMCCSQFGYCGKGPKYCGR") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSSSCCSTTCEECTTSCEESSHHHHCC", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CccCCCCCCCcccccceeCCchHhhCc", ) self.assertEqual( alignment.column_annotations["Confidence"], " 345689999999999999999999973", ) self.assertEqual( str(alignment), """\ 1mmc_A 3 CVRGRCPSGMCCSQFGYCGKGPKYCGR 30 0 .....||...||||.||||.|..|||. 27 2UVO:A|PD 6 GSNMECPNNLCCSQYGYCGMGGDYCGK 33 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 3, 30], [ 6, 33]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'V', 'R', 'G', 'R', 'C', 'P', 'S', 'G', 'M', 'C', 'C', 'S', 'Q', 'F', 'G', 'Y', 'C', 'G', 'K', 'G', 'P', 'K', 'Y', 'C', 'G', 'R'], ['G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 96.90) self.assertAlmostEqual(alignment.annotations["E-value"], 1.3e-06) self.assertAlmostEqual(alignment.annotations["Score"], 43.64) self.assertAlmostEqual(alignment.annotations["Identities"], 48) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.477) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 20.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual(alignment.query.seq[95:118], "KLCPNNLCCSQWGFCGLGSEFCG") self.assertEqual(alignment[1], "KLCPNNLCCSQWGFCGLGSEFCG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~c~~~~CCS~~G~CG~~~~~C~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~C~~~~CCs~~G~CGtt~~~C~", ) self.assertEqual(alignment.target.id, "2n1s_A") self.assertEqual(alignment.target.seq[7:30], "GRCSGGLCCSKYGYCGSGPAYCG") self.assertEqual(alignment.target.annotations["hmm_name"], "2n1s_A") self.assertEqual( alignment.target.annotations["hmm_description"], "AMP-2; antimicrobial peptide, ICK, cystine knot inhibitor, cystine antimicrobial protein; NMR {Stellaria media}", ) self.assertEqual(alignment[0], "GRCSGGLCCSKYGYCGSGPAYCG") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " TBCSTTCEECTTSBEECSHHHHC", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCccccccccCcchhhcC", ) self.assertEqual( alignment.column_annotations["Confidence"], " 36888999999999999999985", ) self.assertEqual( str(alignment), """\ 2n1s_A 7 GRCSGGLCCSKYGYCGSGPAYCG 30 0 ..|...||||..|.||.|...|| 23 2UVO:A|PD 95 KLCPNNLCCSQWGFCGLGSEFCG 118 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 7, 30], [ 95, 118]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'R', 'C', 'S', 'G', 'G', 'L', 'C', 'C', 'S', 'K', 'Y', 'G', 'Y', 'C', 'G', 'S', 'G', 'P', 'A', 'Y', 'C', 'G'], ['K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 96.77) self.assertAlmostEqual(alignment.annotations["E-value"], 2.3e-06) self.assertAlmostEqual(alignment.annotations["Score"], 42.68) self.assertAlmostEqual(alignment.annotations["Identities"], 56) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.468) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 23.6) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual(alignment.query.seq[1:32], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCG") self.assertEqual(alignment[1], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~cg~~~C~~~~CCs~~G~CGtt~~~C~", ) self.assertEqual(alignment.target.id, "2n1s_A") self.assertEqual(alignment.target.seq[3:30], "QCYRGRCSGGLCCSKYGYCGSGPAYCG") self.assertEqual(alignment.target.annotations["hmm_name"], "2n1s_A") self.assertEqual( alignment.target.annotations["hmm_description"], "AMP-2; antimicrobial peptide, ICK, cystine knot inhibitor, cystine antimicrobial protein; NMR {Stellaria media}", ) self.assertEqual(alignment[0], "QCY----RGRCSGGLCCSKYGYCGSGPAYCG") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " BCBTTBCSTTCEECTTSBEECSHHHHC", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " hcCCCCCCCCCccccccccCcchhhcC", ) self.assertEqual( alignment.column_annotations["Confidence"], " 566258999999999999999999985", ) self.assertEqual( str(alignment), """\ 2n1s_A 3 QCY----RGRCSGGLCCSKYGYCGSGPAYCG 30 0 .|.----...|...||||.|||||.|..||| 31 2UVO:A|PD 1 RCGEQGSNMECPNNLCCSQYGYCGMGGDYCG 32 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 3, 6, 6, 30], [ 1, 4, 8, 32]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['Q', 'C', 'Y', '-', '-', '-', '-', 'R', 'G', 'R', 'C', 'S', 'G', 'G', 'L', 'C', 'C', 'S', 'K', 'Y', 'G', 'Y', 'C', 'G', 'S', 'G', 'P', 'A', 'Y', 'C', 'G'], ['R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 96.11) self.assertAlmostEqual(alignment.annotations["E-value"], 2.5e-05) self.assertAlmostEqual(alignment.annotations["Score"], 59.25) self.assertAlmostEqual(alignment.annotations["Identities"], 66) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.556) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 32.2) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[86:124], "IKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG" ) self.assertEqual(alignment[1], "IKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~cG~~~~~~~c~~~~ccs~~g~cg~~~~~C~~~cq~~ ", ) self.assertEqual(alignment.target.id, "2dkv_A") self.assertEqual( alignment.target.seq[1:39], "EQCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "2dkv_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Chitinase; whole structure, oryza sativa L. japonica, hydrolase; HET: MES; 2.00A {Oryza sativa japonica group} PDB: 3iwr_A*", ) self.assertEqual(alignment[0], "EQCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CBCSTTTTTCCCGGGCEECTTSBEESSHHHHSTTCCBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCcCCCCCeeCcCCcccCCccccCccccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 35666555578999999999999999999999999975 ", ) self.assertEqual( str(alignment), """\ 2dkv_A 1 EQCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQ 39 0 ..||.||||..|||.||||.||.||..|.|||.||||. 38 2UVO:A|PD 86 IKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 39], [ 86, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'Q', 'C', 'G', 'A', 'Q', 'A', 'G', 'G', 'A', 'R', 'C', 'P', 'N', 'C', 'L', 'C', 'C', 'S', 'R', 'W', 'G', 'W', 'C', 'G', 'T', 'T', 'S', 'D', 'F', 'C', 'G', 'D', 'G', 'C', 'Q', 'S', 'Q'], ['I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 95.96) self.assertAlmostEqual(alignment.annotations["E-value"], 3.8e-05) self.assertAlmostEqual(alignment.annotations["Score"], 58.17) self.assertAlmostEqual(alignment.annotations["Identities"], 53) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.380) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 33.1) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[43:81], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGG" ) self.assertEqual(alignment[1], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~cG~~~~~~~c~~~~ccs~~g~cg~~~~~C~~~cq~~ ", ) self.assertEqual(alignment.target.id, "2dkv_A") self.assertEqual( alignment.target.seq[1:39], "EQCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "2dkv_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Chitinase; whole structure, oryza sativa L. japonica, hydrolase; HET: MES; 2.00A {Oryza sativa japonica group} PDB: 3iwr_A*", ) self.assertEqual(alignment[0], "EQCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CBCSTTTTTCCCGGGCEECTTSBEESSHHHHSTTCCBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCcCCCCCeeCcCCcccCCccccCccccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 46777666678999999999999999999999999865 ", ) self.assertEqual( str(alignment), """\ 2dkv_A 1 EQCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQ 39 0 ..||.|||||.|.|..|||..|.||.....||.|||.. 38 2UVO:A|PD 43 KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGG 81 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 39], [43, 81]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'Q', 'C', 'G', 'A', 'Q', 'A', 'G', 'G', 'A', 'R', 'C', 'P', 'N', 'C', 'L', 'C', 'C', 'S', 'R', 'W', 'G', 'W', 'C', 'G', 'T', 'T', 'S', 'D', 'F', 'C', 'G', 'D', 'G', 'C', 'Q', 'S', 'Q'], ['K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 85.64) self.assertAlmostEqual(alignment.annotations["E-value"], 0.043) self.assertAlmostEqual(alignment.annotations["Score"], 38.99) self.assertAlmostEqual(alignment.annotations["Identities"], 41) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.195) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual(alignment.query.seq[143:165], "NYCCSKWGSCGIGPGYCGAGCQ") self.assertEqual(alignment[1], "NYCCSKWGSCGIGPGYCG-AGCQ") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~CCS~~G~CG~~~~~C~~gCq ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~CCs~~~~Cg~~~~~C~~~~c~ ", ) self.assertEqual(alignment.target.id, "4zxm_A") self.assertEqual(alignment.target.seq[47:70], "DHCCSEWGWCGRETSHCTCSSCV") self.assertEqual(alignment.target.annotations["hmm_name"], "4zxm_A") self.assertEqual( alignment.target.annotations["hmm_description"], "PGRP domain of peptidoglycan recognition protein; amidase, hydrolase; 2.80A {Branchiostoma belcheri tsingtauense}", ) self.assertEqual(alignment[0], "DHCCSEWGWCGRETSHCTCSSCV") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCeEeCCCCCcCCcccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 689999999999999997 3565 ", ) self.assertEqual( str(alignment), """\ 4zxm_A 47 DHCCSEWGWCGRETSHCTCSSCV 70 0 ..|||.||.||.....|.-..|. 23 2UVO:A|PD 143 NYCCSKWGSCGIGPGYCG-AGCQ 165 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 47, 65, 66, 70], [143, 161, 161, 165]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['D', 'H', 'C', 'C', 'S', 'E', 'W', 'G', 'W', 'C', 'G', 'R', 'E', 'T', 'S', 'H', 'C', 'T', 'C', 'S', 'S', 'C', 'V'], ['N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', '-', 'A', 'G', 'C', 'Q']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 80.97) self.assertAlmostEqual(alignment.annotations["E-value"], 0.11) self.assertAlmostEqual(alignment.annotations["Score"], 32.66) self.assertAlmostEqual(alignment.annotations["Identities"], 20) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.658) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 91.1) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[10:166], "ECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQS", ) self.assertEqual( alignment[1], "ECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQS", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~c~~~~CCs~~g~CG~~~~~c~~~c~~~~c~~~~~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~~c~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~gCq~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~c~~~~cc~~~~~c~~~~~~c~~~c~~~~c~~~~~c~~~~~~c~~~~cc~~~~~c~~~~~~c~~~c~~~~c~~~~~c~~~~~~c~~~~cc~~~~~c~~~~~~c~~~c~~~~c~~~~~c~~~~~~c~~~~cc~~~~~c~~~~~~c~~~c~~ ", ) self.assertEqual(alignment.target.id, "1wga") self.assertEqual( alignment.target.seq[10:160], "XCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXXXXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXXXXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXXXXXCXXXXCCXXXXXCXXXXXXCXXXCXX", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1wga") self.assertEqual( alignment.target.annotations["hmm_description"], "; lectin (agglutinin); NMR {}", ) self.assertEqual( alignment[0], "XCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXX", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 456667777777777777777665554434333344332235666778877777777777776665544333333343323456667788888888777777776665544433334443234566677888777787777777665543 ", ) self.assertEqual( str(alignment), """\ 1wga 10 XCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXX 0 .|....||.....|......|...|....|.....|...--...|....||.....|... 2UVO:A|PD 10 ECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFG 1wga 68 XXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXX 60 ...|...|....|.....|...--...|....||.....|......|...|....|.... 2UVO:A|PD 70 AEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDK 1wga 126 XCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXX 160 120 .|...--...|....||.....|......|...|.. 156 2UVO:A|PD 130 PCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQS 166 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 10, 49, 49, 90, 90, 131, 131, 160], [ 10, 49, 51, 92, 94, 135, 137, 166]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', '-', '-', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', '-', '-', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', '-', '-', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X'], ['E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 80.29) self.assertAlmostEqual(alignment.annotations["E-value"], 0.11) self.assertAlmostEqual(alignment.annotations["Score"], 36.76) self.assertAlmostEqual(alignment.annotations["Identities"], 37) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.967) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:36], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQ" ) self.assertEqual(alignment[1], "RCGEQG-----SNMECPN---NLCCSQYGYCGMGGDYCGK-GCQ") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~Cg~~~~~~~~~~~~C~~~~~~~CCs~~~~Cg~~~~~C~~~~c~ ", ) self.assertEqual(alignment.target.id, "4zxm_A") self.assertEqual( alignment.target.seq[26:70], "RCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCTCSSCV" ) self.assertEqual(alignment.target.annotations["hmm_name"], "4zxm_A") self.assertEqual( alignment.target.annotations["hmm_description"], "PGRP domain of peptidoglycan recognition protein; amidase, hydrolase; 2.80A {Branchiostoma belcheri tsingtauense}", ) self.assertEqual(alignment[0], "RCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCTCSSCV") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCCCCcccCCCCCCCCCCCCCeEeCCCCCcCCcccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 577654 2346765 7899999999999999974 576 ", ) self.assertEqual( str(alignment), """\ 4zxm_A 26 RCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCTCSSCV 70 0 |||...-----...||..---..|||..|.||.....|..-.|. 44 2UVO:A|PD 1 RCGEQG-----SNMECPN---NLCCSQYGYCGMGGDYCGK-GCQ 36 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[26, 32, 37, 44, 47, 66, 67, 70], [ 1, 7, 7, 14, 14, 33, 33, 36]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'C', 'G', 'P', 'N', 'Y', 'P', 'A', 'P', 'D', 'A', 'N', 'P', 'G', 'E', 'C', 'N', 'P', 'H', 'A', 'V', 'D', 'H', 'C', 'C', 'S', 'E', 'W', 'G', 'W', 'C', 'G', 'R', 'E', 'T', 'S', 'H', 'C', 'T', 'C', 'S', 'S', 'C', 'V'], ['R', 'C', 'G', 'E', 'Q', 'G', '-', '-', '-', '-', '-', 'S', 'N', 'M', 'E', 'C', 'P', 'N', '-', '-', '-', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', '-', 'G', 'C', 'Q']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 80.27) self.assertAlmostEqual(alignment.annotations["E-value"], 0.11) self.assertAlmostEqual(alignment.annotations["Score"], 36.29) self.assertAlmostEqual(alignment.annotations["Identities"], 38) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.185) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 19.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual(alignment.query.seq[99:123], "NNLCCSQWGFCGLGSEFCGGGCQS") self.assertEqual(alignment[1], "NNLCCSQWGFCGLGSEFCGG-GCQS") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~CCS~~G~CG~~~~~C~~~Cq~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~CCs~~~~cg~~~~~c~~~~c~d ", ) self.assertEqual(alignment.target.id, "4z8i_A") self.assertEqual(alignment.target.seq[29:54], "VDHCCSEWGWCGRETSHCTCSSCVD") self.assertEqual(alignment.target.annotations["hmm_name"], "4z8i_A") self.assertEqual( alignment.target.annotations["hmm_description"], "BBTPGRP3, peptidoglycan recognition protein 3; chitin-binding domain, AM hydrolase; 2.70A {Branchiostoma belcheri tsingtauense}", ) self.assertEqual(alignment[0], "VDHCCSEWGWCGRETSHCTCSSCVD") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " SCCEECTTSBEECSHHHHHSTTCEE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCEEeCCcccccCCcccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 36899999999999999983 5553 ", ) self.assertEqual( str(alignment), """\ 4z8i_A 29 VDHCCSEWGWCGRETSHCTCSSCVD 54 0 ...|||.||.||.....|..-.|.. 25 2UVO:A|PD 99 NNLCCSQWGFCGLGSEFCGG-GCQS 123 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 29, 49, 50, 54], [ 99, 119, 119, 123]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['V', 'D', 'H', 'C', 'C', 'S', 'E', 'W', 'G', 'W', 'C', 'G', 'R', 'E', 'T', 'S', 'H', 'C', 'T', 'C', 'S', 'S', 'C', 'V', 'D'], ['N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', '-', 'G', 'C', 'Q', 'S']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 79.58) self.assertAlmostEqual(alignment.annotations["E-value"], 0.12) self.assertAlmostEqual(alignment.annotations["Score"], 36.06) self.assertAlmostEqual(alignment.annotations["Identities"], 35) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.927) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 27.4) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:37], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQN" ) self.assertEqual(alignment[1], "ERCGEQG-----SNMECPN---NLCCSQYGYCGMGGDYCGK-GCQN") self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~c~~~c~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~rCg~~~~~~~~~~~~C~~~~~~~CCs~~~~cg~~~~~c~~~~c~d ", ) self.assertEqual(alignment.target.id, "4z8i_A") self.assertEqual( alignment.target.seq[8:54], "GRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCTCSSCVD" ) self.assertEqual(alignment.target.annotations["hmm_name"], "4z8i_A") self.assertEqual( alignment.target.annotations["hmm_description"], "BBTPGRP3, peptidoglycan recognition protein 3; chitin-binding domain, AM hydrolase; 2.70A {Branchiostoma belcheri tsingtauense}", ) self.assertEqual(alignment[0], "GRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCTCSSCVD") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " SBCBSSSCBTTBSSBBCCTTSSCCEECTTSBEECSHHHHHSTTCEE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCCCCCcccCCCCCCCCCCCCCEEeCCcccccCCcccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 3677664 3345653 7899999999999999984 5654 ", ) self.assertEqual( str(alignment), """\ 4z8i_A 8 GRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCTCSSCVD 54 0 .|||...-----...||..---..|||..|.||.....|..-.|.. 46 2UVO:A|PD 0 ERCGEQG-----SNMECPN---NLCCSQYGYCGMGGDYCGK-GCQN 37 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 8, 15, 20, 27, 30, 49, 50, 54], [ 0, 7, 7, 14, 14, 33, 33, 37]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'R', 'C', 'G', 'P', 'N', 'Y', 'P', 'A', 'P', 'D', 'A', 'N', 'P', 'G', 'E', 'C', 'N', 'P', 'H', 'A', 'V', 'D', 'H', 'C', 'C', 'S', 'E', 'W', 'G', 'W', 'C', 'G', 'R', 'E', 'T', 'S', 'H', 'C', 'T', 'C', 'S', 'S', 'C', 'V', 'D'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', '-', '-', '-', '-', '-', 'S', 'N', 'M', 'E', 'C', 'P', 'N', '-', '-', '-', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', '-', 'G', 'C', 'Q', 'N']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 40.43) self.assertAlmostEqual(alignment.annotations["E-value"], 2.6) self.assertAlmostEqual(alignment.annotations["Score"], 25.90) self.assertAlmostEqual(alignment.annotations["Identities"], 20) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.652) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 54.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[53:163], "TCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAG", ) self.assertEqual( alignment[1], "TCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~c~~~~CCs~~g~CG~~~~~c~~~c~~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~Cq~~~c~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~g ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~c~~~~cc~~~~~c~~~~~~c~~~c~~~~c~~~~~c~~~~~~c~~~~cc~~~~~c~~~~~~c~~~c~~~~c~~~~~c~~~~~~c~~~~cc~~~~~c~~~~~~c~~~ ", ) self.assertEqual(alignment.target.id, "1wga") self.assertEqual( alignment.target.seq[10:116], "XCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXXXXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXXXXXCXXXXCCXXXXXCXXXXXXCXXX", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1wga") self.assertEqual( alignment.target.annotations["hmm_description"], "; lectin (agglutinin); NMR {}", ) self.assertEqual( alignment[0], "XCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXX", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 3445566666666666665665555433332233333212346666777777777777666666555443322233332223344455555555555555544433 ", ) self.assertEqual( str(alignment), """\ 1wga 10 XCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXX 0 .|....||.....|......|...|....|.....|...--...|....||.....|... 2UVO:A|PD 53 TCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLG 1wga 68 XXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXX 116 60 ...|...|....|.....|...--...|....||.....|......|... 110 2UVO:A|PD 113 SEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAG 163 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 10, 49, 49, 90, 90, 116], [ 53, 92, 94, 135, 137, 163]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', '-', '-', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', '-', '-', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X'], ['T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_length(self): """Test getting the number of alignments without parsing the file.""" stream = open(self.path) alignments = Align.parse(stream, "hhr") stream.close() self.assertEqual(len(alignments), 32) class Align_hhr_2uvo_hhsearch(unittest.TestCase): path = os.path.join("HHsuite", "2uvo_hhsearch.hhr") def test_reading(self): alignments = Align.parse(self.path, "hhr") self.assertEqual(alignments.metadata["No_of_seqs"], (1, 4)) self.assertAlmostEqual(alignments.metadata["Neff"], 1.0) self.assertEqual(alignments.metadata["Searched_HMMs"], 38388) self.assertEqual(alignments.metadata["Rundate"], "Fri Feb 1 13:49:32 2019") self.assertEqual( alignments.metadata["Command line"], "hhsearch -i 2uvo.fasta -d /pdb70_hhm_db", ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 4.6e-42, places=43) self.assertAlmostEqual(alignment.annotations["Score"], 249.39) self.assertAlmostEqual(alignment.annotations["Identities"], 100) self.assertAlmostEqual(alignment.annotations["Similarity"], 2.050) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 166.9) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:171], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG", ) self.assertEqual( alignment[1], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "ercgeqgsnmecpnnlccsqygycgmggdycgkgcqngacwtskrcgsqaggatctnnqccsqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgacstdkpcgkdaggrvctnnyccskwgscgigpgycgagcqsggcdg", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~~cg~~~~~~~c~~~~CCS~~g~Cg~~~~~Cg~gC~~~~c~~~~~cg~~~~~~~c~~~~CCs~~g~Cg~~~~~c~~~c~~~~~~~~~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~C~~gCq~~~c~~~~~cg~~~~~~~c~~~~ccs~~g~Cg~~~~~C~~~cq~~~~~~", ) self.assertEqual(alignment.target.id, "2uvo_A") self.assertEqual( alignment.target.seq[0:171], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG", ) self.assertEqual(alignment.target.annotations["hmm_name"], "2uvo_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Agglutinin isolectin 1; carbohydrate-binding protein, hevein domain, chitin-binding, GERM agglutinin, chitin-binding protein; HET: NDG NAG GOL; 1.40A {Triticum aestivum} PDB: 1wgc_A* 2cwg_A* 2x3t_A* 4aml_A* 7wga_A 9wga_A 2wgc_A 1wgt_A 1k7t_A* 1k7v_A* 1k7u_A 2x52_A* 1t0w_A*", ) self.assertEqual( alignment[0], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CBCBGGGTTBBCGGGCEECTTSBEEBSHHHHSTTCCBSSCSSCCBCBGGGTTBCCSTTCEECTTSBEEBSHHHHSTTCCBSSCSSCCBCBGGGTTBCCGGGCEECTTSBEEBSHHHHSTTCCBSSCSSCCCCBTTTTTBCCSTTCEECTTSCEEBSHHHHSTTCCBSSCC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCCCCCCCCcCCCCCCeeCCCCeECCCcccccCCccccccccccccCcccCCcccCCccccCCCceeCCCccccCCCcccccccccccccccccCCCCCCCcccCCCCccCCCcccccCCCcCCccccccccccccccccCCCCCCcCCCCEecCchhhcccccccCCCCC", ) self.assertEqual( alignment.column_annotations["Confidence"], "799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999998899999999999999999999999999999999999999999999999999999999999999999999999999986", ) self.assertEqual( str(alignment), """\ 2uvo_A 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQC 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 2UVO:A|PD 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQC 2uvo_A 60 CSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 2UVO:A|PD 60 CSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG 2uvo_A 120 CQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171 120 ||||||||||||||||||||||||||||||||||||||||||||||||||| 171 2UVO:A|PD 120 CQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 171], [ 0, 171]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G', 'G', 'C', 'D', 'G'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G', 'G', 'C', 'D', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.95) self.assertAlmostEqual(alignment.annotations["E-value"], 2.8e-33, places=34) self.assertAlmostEqual(alignment.annotations["Score"], 204.56) self.assertAlmostEqual(alignment.annotations["Identities"], 49) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.252) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 153.2) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:169], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC", ) self.assertEqual( alignment[1], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " rcgeqgsnmecpnnlccsqygycgmggdycgkgcqngacwtskrcgsqaggatctnnqccsqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgacstdkpcgkdaggrvctnnyccskwgscgigpgycgagcqsggc ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~g~~~~~~~c~~~~CCs~~g~Cg~~~~~c~~~C~~~~c~~~~~cg~~~~~c~~~~CCs~~G~CG~~~~~C~~~C~~~~~~~~~~Cg~~~~~c~~~~Ccs~~G~CGt~~~~C~~~cq~~~c~~~~~cg~~~~~c~~~~Ccs~~g~Cg~~~~~C~~~cq~~~~ ", ) self.assertEqual(alignment.target.id, "2wga") self.assertEqual( alignment.target.seq[1:163], "GXGCXGXXMYCSTNNCCXXWESCGSGGYXCGEGCNLGACQXGXPCXXPGSVCTNLHCCARGGHCGMGSGYCGXGCXGGACXADIXCGXGXXXCPTDSCCGGWGXCGNGXEFCGXGCXVGGCAAXSPCGXPGSXCTLDKCCSGXGACXSGSGGCGXGCXAGGC", ) self.assertEqual(alignment.target.annotations["hmm_name"], "2wga") self.assertEqual( alignment.target.annotations["hmm_description"], "; lectin (agglutinin); NMR {}", ) self.assertEqual( alignment[0], "GXGCXGXXMYCSTNNCCXXWESCGSGGYXCGEGCNLGACQXGXPCXX--PGSVCTNLHCCARGGHCGMGSGYCGXGCXGGACXADIXCGXG--XXXCPTDSCCGGWGXCGNGXEFCGXGCXVGGCAAXSPCGX--PGSXCTLDKCCSGXGACXSGSGGCGXGCXAGGC", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSGGGSSCCCCSTTCEECTTSCEECSTTTTSTTCCSSSCSSCCCSSSSSCCCSTTCEECTTSCEESSHHHHSSCCSSSSCSSCCCCTTSSSCCSTTCBCCSSSCCBCSHHHHSTTCCSSSCSSCCCCSSSCCCCSTTCEECSSSSEECSTTTTSSCCSSSSC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ccCCCcccccCCCCceECCcceECCCCccccCccccCcccccceeccCCCcCCCCcccCCCceeCCCCcccCCCccccccccccccCcccccCCCCCccCCCCCccCccccccCCccccccccccccCCCcccCCcccccCCCCceeCCccccCCCCcCCCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 588899999999999999999999999999999999999999999985789999999999999999999999999999999999999855679999999999999999999999999999999999988367899999999999999999999999999876 ", ) self.assertEqual( str(alignment), """\ 2wga 1 GXGCXGXXMYCSTNNCCXXWESCGSGGYXCGEGCNLGACQXGXPCXX--PGSVCTNLHCC 0 ..|..|..|.|..|.||.....||.||..||.||..|||.....|..--.|..|||..|| 2UVO:A|PD 1 RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCC 2wga 59 ARGGHCGMGSGYCGXGCXGGACXADIXCGXG--XXXCPTDSCCGGWGXCGNGXEFCGXGC 60 ...|.||.|..|||.||.||.|.|||.||..--...||...||..||.||.|.||||.|| 2UVO:A|PD 61 SQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGC 2wga 117 XVGGCAAXSPCGX--PGSXCTLDKCCSGXGACXSGSGGCGXGCXAGGC 163 120 ..|.|....|||.--.|..||...|||..|.|..|.|.||.||..||| 168 2UVO:A|PD 121 QSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC 169 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 48, 48, 90, 90, 130, 130, 163], [ 1, 48, 50, 92, 94, 134, 136, 169]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'X', 'G', 'C', 'X', 'G', 'X', 'X', 'M', 'Y', 'C', 'S', 'T', 'N', 'N', 'C', 'C', 'X', 'X', 'W', 'E', 'S', 'C', 'G', 'S', 'G', 'G', 'Y', 'X', 'C', 'G', 'E', 'G', 'C', 'N', 'L', 'G', 'A', 'C', 'Q', 'X', 'G', 'X', 'P', 'C', 'X', 'X', '-', '-', 'P', 'G', 'S', 'V', 'C', 'T', 'N', 'L', 'H', 'C', 'C', 'A', 'R', 'G', 'G', 'H', 'C', 'G', 'M', 'G', 'S', 'G', 'Y', 'C', 'G', 'X', 'G', 'C', 'X', 'G', 'G', 'A', 'C', 'X', 'A', 'D', 'I', 'X', 'C', 'G', 'X', 'G', '-', '-', 'X', 'X', 'X', 'C', 'P', 'T', 'D', 'S', 'C', 'C', 'G', 'G', 'W', 'G', 'X', 'C', 'G', 'N', 'G', 'X', 'E', 'F', 'C', 'G', 'X', 'G', 'C', 'X', 'V', 'G', 'G', 'C', 'A', 'A', 'X', 'S', 'P', 'C', 'G', 'X', '-', '-', 'P', 'G', 'S', 'X', 'C', 'T', 'L', 'D', 'K', 'C', 'C', 'S', 'G', 'X', 'G', 'A', 'C', 'X', 'S', 'G', 'S', 'G', 'G', 'C', 'G', 'X', 'G', 'C', 'X', 'A', 'G', 'G', 'C'], ['R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G', 'G', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.84) self.assertAlmostEqual(alignment.annotations["E-value"], 1.1e-25, places=26) self.assertAlmostEqual(alignment.annotations["Score"], 163.39) self.assertAlmostEqual(alignment.annotations["Identities"], 60) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.533) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 121.1) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[43:169], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC", ) self.assertEqual( alignment[1], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " krcgsqaggatctnnqccsqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgacstdkpcgkdaggrvctnnyccskwgscgigpgycgagcqsggc ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~~cg~~~~~~~c~~~~CCS~~g~Cg~~~~~Cg~gC~~~~c~~~~~cg~~~~~~~c~~~~CCs~~g~Cg~~~~~c~~~c~~~~~~~~~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~C~~gCq~~~c ", ) self.assertEqual(alignment.target.id, "2uvo_A") self.assertEqual( alignment.target.seq[0:126], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGAC", ) self.assertEqual(alignment.target.annotations["hmm_name"], "2uvo_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Agglutinin isolectin 1; carbohydrate-binding protein, hevein domain, chitin-binding, GERM agglutinin, chitin-binding protein; HET: NDG NAG GOL; 1.40A {Triticum aestivum} PDB: 1wgc_A* 2cwg_A* 2x3t_A* 4aml_A* 7wga_A 9wga_A 2wgc_A 1wgt_A 1k7t_A* 1k7v_A* 1k7u_A 2x52_A* 1t0w_A*", ) self.assertEqual( alignment[0], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGAC", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CBCBGGGTTBBCGGGCEECTTSBEEBSHHHHSTTCCBSSCSSCCBCBGGGTTBCCSTTCEECTTSBEEBSHHHHSTTCCBSSCSSCCBCBGGGTTBCCGGGCEECTTSBEEBSHHHHSTTCCBSSC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCCCCCCCCcCCCCCCeeCCCCeECCCcccccCCccccccccccccCcccCCcccCCccccCCCceeCCCccccCCCcccccccccccccccccCCCCCCCcccCCCCccCCCcccccCCCcCCcc ", ) self.assertEqual( alignment.column_annotations["Confidence"], "489999999999999999999999999999999999999999999999998899999999999999999999999999999999999999988889999999999999999999999999998644 ", ) self.assertEqual( str(alignment), """\ 2uvo_A 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQC 0 .|||.|.....|.||.|||||||||.|..|||.|||.|.|.....|||||||..|.||.| 2UVO:A|PD 43 KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLC 2uvo_A 60 CSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG 60 |||.|.||.|.|.||.|||.|.|..|..||..|||..|.||.|||.||.||.|...||.| 2UVO:A|PD 103 CSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAG 2uvo_A 120 CQSGAC 126 120 ||||.| 126 2UVO:A|PD 163 CQSGGC 169 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 126], [ 43, 169]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C'], ['K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G', 'G', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.84) self.assertAlmostEqual(alignment.annotations["E-value"], 1.5e-25, places=26) self.assertAlmostEqual(alignment.annotations["Score"], 157.96) self.assertAlmostEqual(alignment.annotations["Identities"], 52) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.251) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 110.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[43:167], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSG", ) self.assertEqual( alignment[1], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " krcgsqaggatctnnqccsqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgacstdkpcgkdaggrvctnnyccskwgscgigpgycgagcqsg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~cg~~~~~~~c~~g~CCs~~g~CG~~~~~Cg~gCq~~c~~~~Cg~~~~~~~c~~~~CCs~~G~CG~~~~~C~~~Cq~~c~~~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~C~~gCq~~ ", ) self.assertEqual(alignment.target.id, "1ulk_A") self.assertEqual( alignment.target.seq[1:121], "PVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQCDYNRCGKEFGGKECHDELCCSQYGWCGNSDGHCGEGCQSQCSYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDGCQSQ", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1ulk_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Lectin-C; chitin-binding protein, hevein domain, PL-C, sugar binding protein; 1.80A {Phytolacca americana} SCOP: g.3.1.1 g.3.1.1 g.3.1.1", ) self.assertEqual( alignment[0], "PVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQ-CD-YNRCGKEFGGKECHDELCCSQYGWCGNSDGHCGEGCQSQ-C-SYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDGCQSQ", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCSBGGGTTBCCGGGCEECTTSCEESSHHHHSTTCCBCTTTTBCBGGGTTBCCGGGCEECTTSBEECSHHHHSTTCCBCTTTTBCBGGGTTBCCSTTCEECTTSBEECSHHHHSTTCCBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CcCcCCCCCCCCCCCCeECCCCeeCCCccccCCCccccceeeeccccccCCCCCCccccCCCcccccCcccccCCcccccCcccccccCCCccCCCCcccccCceecCcccccCcccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 699999999999999999999999999999999999764355788888889999999999999999999999999998633578999888999999999999999999999999999984 ", ) self.assertEqual( str(alignment), """\ 1ulk_A 1 PVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQ-CD-YNRCGKEFGGKECHDELC 0 ..||..|.|..|....||||.||||...||||.|||..-|.-...||...|||.|...|| 2UVO:A|PD 43 KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLC 1ulk_A 59 CSQYGWCGNSDGHCGEGCQSQ-C-SYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDG 60 |||.|.||.....||.||||.-|-....||||.|||.||...|||..|.||.....|..| 2UVO:A|PD 103 CSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAG 1ulk_A 117 CQSQ 121 120 |||. 124 2UVO:A|PD 163 CQSG 167 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 39, 39, 41, 41, 80, 80, 81, 81, 121], [ 43, 81, 82, 84, 85, 124, 125, 126, 127, 167]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['P', 'V', 'C', 'G', 'V', 'R', 'A', 'S', 'G', 'R', 'V', 'C', 'P', 'D', 'G', 'Y', 'C', 'C', 'S', 'Q', 'W', 'G', 'Y', 'C', 'G', 'T', 'T', 'E', 'E', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'S', 'Q', '-', 'C', 'D', '-', 'Y', 'N', 'R', 'C', 'G', 'K', 'E', 'F', 'G', 'G', 'K', 'E', 'C', 'H', 'D', 'E', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'W', 'C', 'G', 'N', 'S', 'D', 'G', 'H', 'C', 'G', 'E', 'G', 'C', 'Q', 'S', 'Q', '-', 'C', '-', 'S', 'Y', 'W', 'R', 'C', 'G', 'K', 'D', 'F', 'G', 'G', 'R', 'L', 'C', 'T', 'E', 'D', 'M', 'C', 'C', 'S', 'Q', 'Y', 'G', 'W', 'C', 'G', 'L', 'T', 'D', 'D', 'H', 'C', 'E', 'D', 'G', 'C', 'Q', 'S', 'Q'], ['K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.82) self.assertAlmostEqual(alignment.annotations["E-value"], 6.5e-25, places=26) self.assertAlmostEqual(alignment.annotations["Score"], 154.69) self.assertAlmostEqual(alignment.annotations["Identities"], 50) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.299) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 109.2) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:123], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQS", ) self.assertEqual( alignment[1], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQS", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "ercgeqgsnmecpnnlccsqygycgmggdycgkgcqngacwtskrcgsqaggatctnnqccsqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqs ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~cg~~~~~~~c~~g~CCs~~g~CG~~~~~Cg~gCq~~c~~~~Cg~~~~~~~c~~~~CCs~~G~CG~~~~~C~~~Cq~~c~~~~cg~~~~~~~c~~~~CCs~~g~CG~~~~~C~~gCq~ ", ) self.assertEqual(alignment.target.id, "1ulk_A") self.assertEqual( alignment.target.seq[1:120], "PVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQCDYNRCGKEFGGKECHDELCCSQYGWCGNSDGHCGEGCQSQCSYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDGCQS", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1ulk_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Lectin-C; chitin-binding protein, hevein domain, PL-C, sugar binding protein; 1.80A {Phytolacca americana} SCOP: g.3.1.1 g.3.1.1 g.3.1.1", ) self.assertEqual( alignment[0], "PVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQ-CD-YNRCGKEFGGKECHDELCCSQYGWCGNSDGHCGEGCQSQ-CS-YWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDGCQS", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCSBGGGTTBCCGGGCEECTTSCEESSHHHHSTTCCBCTTTTBCBGGGTTBCCGGGCEECTTSBEECSHHHHSTTCCBCTTTTBCBGGGTTBCCSTTCEECTTSBEECSHHHHSTTCCB ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CcCcCCCCCCCCCCCCeECCCCeeCCCccccCCCccccceeeeccccccCCCCCCccccCCCcccccCcccccCCcccccCcccccccCCCccCCCCcccccCceecCcccccCccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 48999999999999999999999999999999999976444589988889999999999999999999999999999753356888888888999999999999999999999999997 ", ) self.assertEqual( str(alignment), """\ 1ulk_A 1 PVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQ-CD-YNRCGKEFGGKECHDELC 0 ..||...|...||...||||.||||....|||||||..-|.-..|||...||..|....| 2UVO:A|PD 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQC 1ulk_A 59 CSQYGWCGNSDGHCGEGCQSQ-CS-YWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDG 60 |||||.||.....||.|||..-|.-...||...||.||....||||.|.|||....|..| 2UVO:A|PD 60 CSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG 1ulk_A 117 CQS 120 120 ||| 123 2UVO:A|PD 120 CQS 123 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 39, 39, 41, 41, 80, 80, 82, 82, 120], [ 0, 38, 39, 41, 42, 81, 82, 84, 85, 123]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['P', 'V', 'C', 'G', 'V', 'R', 'A', 'S', 'G', 'R', 'V', 'C', 'P', 'D', 'G', 'Y', 'C', 'C', 'S', 'Q', 'W', 'G', 'Y', 'C', 'G', 'T', 'T', 'E', 'E', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'S', 'Q', '-', 'C', 'D', '-', 'Y', 'N', 'R', 'C', 'G', 'K', 'E', 'F', 'G', 'G', 'K', 'E', 'C', 'H', 'D', 'E', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'W', 'C', 'G', 'N', 'S', 'D', 'G', 'H', 'C', 'G', 'E', 'G', 'C', 'Q', 'S', 'Q', '-', 'C', 'S', '-', 'Y', 'W', 'R', 'C', 'G', 'K', 'D', 'F', 'G', 'G', 'R', 'L', 'C', 'T', 'E', 'D', 'M', 'C', 'C', 'S', 'Q', 'Y', 'G', 'W', 'C', 'G', 'L', 'T', 'D', 'D', 'H', 'C', 'E', 'D', 'G', 'C', 'Q', 'S'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.78) self.assertAlmostEqual(alignment.annotations["E-value"], 1.7e-23, places=24) self.assertAlmostEqual(alignment.annotations["Score"], 152.97) self.assertAlmostEqual(alignment.annotations["Identities"], 41) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.180) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 114.3) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[44:169], "RCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC", ) self.assertEqual( alignment[1], "RCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " rcgsqaggatctnnqccsqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgacstdkpcgkdaggrvctnnyccskwgscgigpgycgagcqsggc ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~g~~~~~~~c~~~~CCs~~g~Cg~~~~~c~~~C~~~~c~~~~~cg~~~~~c~~~~CCs~~G~CG~~~~~C~~~C~~~~~~~~~~Cg~~~~~c~~~~Ccs~~G~CGt~~~~C~~~cq~~~c ", ) self.assertEqual(alignment.target.id, "2wga") self.assertEqual( alignment.target.seq[1:122], "GXGCXGXXMYCSTNNCCXXWESCGSGGYXCGEGCNLGACQXGXPCXXPGSVCTNLHCCARGGHCGMGSGYCGXGCXGGACXADIXCGXGXXXCPTDSCCGGWGXCGNGXEFCGXGCXVGGC", ) self.assertEqual(alignment.target.annotations["hmm_name"], "2wga") self.assertEqual( alignment.target.annotations["hmm_description"], "; lectin (agglutinin); NMR {}", ) self.assertEqual( alignment[0], "GXGCXGXXMYCSTNNCCXXWESCGSGGYXCGEGCNLGACQXGXPCXX--PGSVCTNLHCCARGGHCGMGSGYCGXGCXGGACXADIXCGXG--XXXCPTDSCCGGWGXCGNGXEFCGXGCXVGGC", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSGGGSSCCCCSTTCEECTTSCEECSTTTTSTTCCSSSCSSCCCSSSSSCCCSTTCEECTTSCEESSHHHHSSCCSSSSCSSCCCCTTSSSCCSTTCBCCSSSCCBCSHHHHSTTCCSSSC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ccCCCcccccCCCCceECCcceECCCCccccCccccCcccccceeccCCCcCCCCcccCCCceeCCCCcccCCCccccccccccccCcccccCCCCCccCCCCCccCccccccCCcccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 4889999999999999999999999999999999999999999999857889999999999999999999999999999999999998667899999999999999999999999998654 ", ) self.assertEqual( str(alignment), """\ 2wga 1 GXGCXGXXMYCSTNNCCXXWESCGSGGYXCGEGCNLGACQXGXPCXX--PGSVCTNLHCC 0 ..|.......|..|.||.....||.|...||.||..|.|.....|..--.|..|.|..|| 2UVO:A|PD 44 RCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCC 2wga 59 ARGGHCGMGSGYCGXGCXGGACXADIXCGXG--XXXCPTDSCCGGWGXCGNGXEFCGXGC 60 ...|.||.||..||.||..|||..|..||..--...|....||..||.||.|...||.|| 2UVO:A|PD 104 SQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGC 2wga 117 XVGGC 122 120 ..||| 125 2UVO:A|PD 164 QSGGC 169 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 48, 48, 90, 90, 122], [ 44, 91, 93, 135, 137, 169]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'X', 'G', 'C', 'X', 'G', 'X', 'X', 'M', 'Y', 'C', 'S', 'T', 'N', 'N', 'C', 'C', 'X', 'X', 'W', 'E', 'S', 'C', 'G', 'S', 'G', 'G', 'Y', 'X', 'C', 'G', 'E', 'G', 'C', 'N', 'L', 'G', 'A', 'C', 'Q', 'X', 'G', 'X', 'P', 'C', 'X', 'X', '-', '-', 'P', 'G', 'S', 'V', 'C', 'T', 'N', 'L', 'H', 'C', 'C', 'A', 'R', 'G', 'G', 'H', 'C', 'G', 'M', 'G', 'S', 'G', 'Y', 'C', 'G', 'X', 'G', 'C', 'X', 'G', 'G', 'A', 'C', 'X', 'A', 'D', 'I', 'X', 'C', 'G', 'X', 'G', '-', '-', 'X', 'X', 'X', 'C', 'P', 'T', 'D', 'S', 'C', 'C', 'G', 'G', 'W', 'G', 'X', 'C', 'G', 'N', 'G', 'X', 'E', 'F', 'C', 'G', 'X', 'G', 'C', 'X', 'V', 'G', 'G', 'C'], ['R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G', 'G', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.54) self.assertAlmostEqual(alignment.annotations["E-value"], 1.1e-18, places=19) self.assertAlmostEqual(alignment.annotations["Score"], 113.58) self.assertAlmostEqual(alignment.annotations["Identities"], 48) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.312) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 73.1) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[43:124], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG", ) self.assertEqual( alignment[1], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " krcgsqaggatctnnqccsqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~cg~~~~~~~C~~g~CCs~~G~Cg~~~~~c~~~c~~~~~~g~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~C~~~Cqs~ ", ) self.assertEqual(alignment.target.id, "1uha_A") self.assertEqual( alignment.target.seq[1:80], "PECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQCDYWRCGRDFGGRLCEEDMCCSKYGWCGYSDDHCEDGCQSQ", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1uha_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Lectin-D2; chitin-binding domain, sugar binding protein; 1.50A {Phytolacca americana} SCOP: g.3.1.1 g.3.1.1 PDB: 1ulm_A* 1uln_A", ) self.assertEqual( alignment[0], "PECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQ-C-DYWRCGRDFGGRLCEEDMCCSKYGWCGYSDDHCEDGCQSQ", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCSBGGGTTBCCGGGCEECTTSCEESSHHHHSTTCCBCTTTTBCBGGGTTBCCSTTCEECTTSBEECSHHHHSTTCCBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCcCCCCCccCCCccccCccccccCCccccccccccccccceecCCCCCccCCCccccCCccccccccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 5899999999999999999999999999999999996534678998888999999999999999999999999999984 ", ) self.assertEqual( str(alignment), """\ 1uha_A 1 PECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQ-C-DYWRCGRDFGGRLCEEDMC 0 ..||..|.|..|.|..||||.||||....|||.|||..-|-....||...||.||....| 2UVO:A|PD 43 KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLC 1uha_A 59 CSKYGWCGYSDDHCEDGCQSQ 80 60 ||..|.||.....|..||||. 81 2UVO:A|PD 103 CSQWGFCGLGSEFCGGGCQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 39, 39, 40, 40, 80], [ 43, 81, 82, 83, 84, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['P', 'E', 'C', 'G', 'E', 'R', 'A', 'S', 'G', 'K', 'R', 'C', 'P', 'N', 'G', 'K', 'C', 'C', 'S', 'Q', 'W', 'G', 'Y', 'C', 'G', 'T', 'T', 'D', 'N', 'Y', 'C', 'G', 'Q', 'G', 'C', 'Q', 'S', 'Q', '-', 'C', '-', 'D', 'Y', 'W', 'R', 'C', 'G', 'R', 'D', 'F', 'G', 'G', 'R', 'L', 'C', 'E', 'E', 'D', 'M', 'C', 'C', 'S', 'K', 'Y', 'G', 'W', 'C', 'G', 'Y', 'S', 'D', 'D', 'H', 'C', 'E', 'D', 'G', 'C', 'Q', 'S', 'Q'], ['K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.54) self.assertAlmostEqual(alignment.annotations["E-value"], 1.2e-18, places=19) self.assertAlmostEqual(alignment.annotations["Score"], 115.94) self.assertAlmostEqual(alignment.annotations["Identities"], 47) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.232) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 74.1) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[44:124], "RCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG", ) self.assertEqual( alignment[1], "RCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRA----DIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG-CQSG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " rcgsqaggatctnnqccsqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~cg~~~~~~~C~~~~CCS~~G~CG~~~~~C~~~Cq~~c~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "1en2_A") self.assertEqual( alignment.target.seq[1:85], "RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYR", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1en2_A") self.assertEqual( alignment.target.annotations["hmm_description"], "UDA, agglutinin isolectin I/agglutinin isolectin V/ AG isolectin VI; hevein domain, superantigen, saccharide binding binding protein; HET: NAG; 1.40A {Urtica dioica} SCOP: g.3.1.1 g.3.1.1 PDB: 1eis_A* 1enm_A* 1ehd_A 1ehh_A* 1iqb_A", ) self.assertEqual( alignment[0], "RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENK-CWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYR", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " BCTTTTTSCCCGGGCEEETTSBEESSHHHHSTTEEESCGGGCCTTCBCSGGGTCCCCCTTCEEETTSBEESSHHHHSGGGEEEC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCccCCCCcccCCCceecccccccCCCCcCCCcccccCCcccCCcccccccCCCCeECCCceECCCccccCCCCcccC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 7999999999999999999999999999999999976665 88999988889999999999999999999999998 9985 ", ) self.assertEqual( str(alignment), """\ 1en2_A 1 RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENK-CWSGERSDHRCGAAVGNPPCGQ 0 |||||.||.||....|||..|.||....|||..|...-|..----|..||...|...|.. 2UVO:A|PD 44 RCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRA----DIKCGSQAGGKLCPN 1en2_A 60 DRCCSVHGWCGGGNDYCSGGNCQYR 85 60 ..|||..|.||.|...|.||-||.. 85 2UVO:A|PD 100 NLCCSQWGFCGLGSEFCGGG-CQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 38, 38, 41, 45, 80, 81, 85], [ 44, 81, 82, 85, 85, 120, 120, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'C', 'G', 'S', 'Q', 'G', 'G', 'G', 'S', 'T', 'C', 'P', 'G', 'L', 'R', 'C', 'C', 'S', 'I', 'W', 'G', 'W', 'C', 'G', 'D', 'S', 'E', 'P', 'Y', 'C', 'G', 'R', 'T', 'C', 'E', 'N', 'K', '-', 'C', 'W', 'S', 'G', 'E', 'R', 'S', 'D', 'H', 'R', 'C', 'G', 'A', 'A', 'V', 'G', 'N', 'P', 'P', 'C', 'G', 'Q', 'D', 'R', 'C', 'C', 'S', 'V', 'H', 'G', 'W', 'C', 'G', 'G', 'G', 'N', 'D', 'Y', 'C', 'S', 'G', 'G', 'N', 'C', 'Q', 'Y', 'R'], ['R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', '-', '-', '-', '-', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', '-', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.41) self.assertAlmostEqual(alignment.annotations["E-value"], 5.1e-17, places=18) self.assertAlmostEqual(alignment.annotations["Score"], 108.07) self.assertAlmostEqual(alignment.annotations["Identities"], 48) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.287) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 74.0) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:81], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGG", ) self.assertEqual( alignment[1], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWT----SKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAG-CQGG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "ercgeqgsnmecpnnlccsqygycgmggdycgkgcqngacwtskrcgsqaggatctnnqccsqygycgfgaeycgagcqgg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~~cg~~~~~~~C~~~~CCS~~G~CG~~~~~C~~~Cq~~c~~~~~~~~~Cg~~~~~~~c~~~~CCS~~G~CG~~~~~C~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "1en2_A") self.assertEqual( alignment.target.seq[0:85], "ERCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYR", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1en2_A") self.assertEqual( alignment.target.annotations["hmm_description"], "UDA, agglutinin isolectin I/agglutinin isolectin V/ AG isolectin VI; hevein domain, superantigen, saccharide binding binding protein; HET: NAG; 1.40A {Urtica dioica} SCOP: g.3.1.1 g.3.1.1 PDB: 1eis_A* 1enm_A* 1ehd_A 1ehh_A* 1iqb_A", ) self.assertEqual( alignment[0], "ERCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENK-CWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYR", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CBCTTTTTSCCCGGGCEEETTSBEESSHHHHSTTEEESCGGGCCTTCBCSGGGTCCCCCTTCEEETTSBEESSHHHHSGGGEEEC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCCCCCCCCccCCCCcccCCCceecccccccCCCCcCCCcccccCCcccCCcccccccCCCCeECCCceECCCccccCCCCcccC ", ) self.assertEqual( alignment.column_annotations["Confidence"], "68999999999999999999999999999999999986764 67899888888999999999999999999999998 8863 ", ) self.assertEqual( str(alignment), """\ 1en2_A 0 ERCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENK-CWSGERSDHRCGAAVGNPPCG 0 ||||.||....||...|||..|.||....|||..|.|.-||.----..|||...|...|. 2UVO:A|PD 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWT----SKRCGSQAGGATCT 1en2_A 59 QDRCCSVHGWCGGGNDYCSGGNCQYR 85 60 ...|||..|.||.|..||..|-||.. 86 2UVO:A|PD 56 NNQCCSQYGYCGFGAEYCGAG-CQGG 81 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 38, 38, 41, 45, 80, 81, 85], [ 0, 38, 39, 42, 42, 77, 77, 81]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'R', 'C', 'G', 'S', 'Q', 'G', 'G', 'G', 'S', 'T', 'C', 'P', 'G', 'L', 'R', 'C', 'C', 'S', 'I', 'W', 'G', 'W', 'C', 'G', 'D', 'S', 'E', 'P', 'Y', 'C', 'G', 'R', 'T', 'C', 'E', 'N', 'K', '-', 'C', 'W', 'S', 'G', 'E', 'R', 'S', 'D', 'H', 'R', 'C', 'G', 'A', 'A', 'V', 'G', 'N', 'P', 'P', 'C', 'G', 'Q', 'D', 'R', 'C', 'C', 'S', 'V', 'H', 'G', 'W', 'C', 'G', 'G', 'G', 'N', 'D', 'Y', 'C', 'S', 'G', 'G', 'N', 'C', 'Q', 'Y', 'R'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', '-', '-', '-', '-', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', '-', 'C', 'Q', 'G', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.38) self.assertAlmostEqual(alignment.annotations["E-value"], 1e-16, places=17) self.assertAlmostEqual(alignment.annotations["Score"], 104.25) self.assertAlmostEqual(alignment.annotations["Identities"], 53) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.284) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 72.3) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[87:167], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSG", ) self.assertEqual( alignment[1], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " kcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgacstdkpcgkdaggrvctnnyccskwgscgigpgycgagcqsg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~cg~~~~~~~C~~g~CCs~~G~Cg~~~~~c~~~c~~~~~~g~Cg~~~~~~~c~~~~CCs~~g~CG~~~~~C~~~Cqs~ ", ) self.assertEqual(alignment.target.id, "1uha_A") self.assertEqual( alignment.target.seq[2:80], "ECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQCDYWRCGRDFGGRLCEEDMCCSKYGWCGYSDDHCEDGCQSQ", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1uha_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Lectin-D2; chitin-binding domain, sugar binding protein; 1.50A {Phytolacca americana} SCOP: g.3.1.1 g.3.1.1 PDB: 1ulm_A* 1uln_A", ) self.assertEqual( alignment[0], "ECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQ--CDYWRCGRDFGGRLCEEDMCCSKYGWCGYSDDHCEDGCQSQ", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSBGGGTTBCCGGGCEECTTSCEESSHHHHSTTCCBCTTTTBCBGGGTTBCCSTTCEECTTSBEECSHHHHSTTCCBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCcCCCCCccCCCccccCccccccCCccccccccccccccceecCCCCCccCCCccccCCccccccccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 588999999999999999999999999999999998624678999889999999999999999999999999999984 ", ) self.assertEqual( str(alignment), """\ 1uha_A 2 ECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQ--CDYWRCGRDFGGRLCEEDMCC 0 .||..|.||.|||..||||||.||.....||.||||.--.....||.|.|||.|....|| 2UVO:A|PD 87 KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCC 1uha_A 60 SKYGWCGYSDDHCEDGCQSQ 80 60 ||.|.||.....|..||||. 80 2UVO:A|PD 147 SKWGSCGIGPGYCGAGCQSG 167 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 39, 39, 80], [ 87, 124, 126, 167]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'C', 'G', 'E', 'R', 'A', 'S', 'G', 'K', 'R', 'C', 'P', 'N', 'G', 'K', 'C', 'C', 'S', 'Q', 'W', 'G', 'Y', 'C', 'G', 'T', 'T', 'D', 'N', 'Y', 'C', 'G', 'Q', 'G', 'C', 'Q', 'S', 'Q', '-', '-', 'C', 'D', 'Y', 'W', 'R', 'C', 'G', 'R', 'D', 'F', 'G', 'G', 'R', 'L', 'C', 'E', 'E', 'D', 'M', 'C', 'C', 'S', 'K', 'Y', 'G', 'W', 'C', 'G', 'Y', 'S', 'D', 'D', 'H', 'C', 'E', 'D', 'G', 'C', 'Q', 'S', 'Q'], ['K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 98.20) self.assertAlmostEqual(alignment.annotations["E-value"], 1.6e-09, places=10) self.assertAlmostEqual(alignment.annotations["Score"], 66.41) self.assertAlmostEqual(alignment.annotations["Identities"], 59) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.390) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 36.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[85:127], "DIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACS" ) self.assertEqual(alignment[1], "DIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACS") self.assertEqual( alignment.query.letter_annotations["Consensus"], " dikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgacs ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~CG~~~~~~~C~~~~CCs~~G~CG~t~~~C~~gCq~~c~ ", ) self.assertEqual(alignment.target.id, "4mpi_A") self.assertEqual( alignment.target.seq[1:42], "MEQCGRQAGGALCPGGLCCSQYGWCANTPEYCGSGCQSQCD" ) self.assertEqual(alignment.target.annotations["hmm_name"], "4mpi_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Class I chitinase; hevein-like domain, chitin oligomers, sugar binding protein; HET: MES; 1.60A {Hevea brasiliensis subsp}", ) self.assertEqual(alignment[0], "MEQCGRQAGGALCPGGLCCSQYGWCANTPEYCGSGCQSQ-CD") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCBCBGGGTTBCCGGGCEECTTSBEECSHHHHSTTCCBCTT ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ccccCCcCCCcccCCCCcCcccceecCCcccccccccccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 45688888889999999999999999999999999998554 ", ) self.assertEqual( str(alignment), """\ 4mpi_A 1 MEQCGRQAGGALCPGGLCCSQYGWCANTPEYCGSGCQSQ-CD 42 0 ...||.||||.|||..|||||.|.|....|.||.||||.-|. 42 2UVO:A|PD 85 DIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACS 127 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 40, 40, 42], [ 85, 124, 125, 127]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['M', 'E', 'Q', 'C', 'G', 'R', 'Q', 'A', 'G', 'G', 'A', 'L', 'C', 'P', 'G', 'G', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'W', 'C', 'A', 'N', 'T', 'P', 'E', 'Y', 'C', 'G', 'S', 'G', 'C', 'Q', 'S', 'Q', '-', 'C', 'D'], ['D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 98.12) self.assertAlmostEqual(alignment.annotations["E-value"], 3.1e-09, places=10) self.assertAlmostEqual(alignment.annotations["Score"], 64.73) self.assertAlmostEqual(alignment.annotations["Identities"], 68) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.600) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 34.0) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[87:124], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG" ) self.assertEqual(alignment[1], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGG--GCQSG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " kcgsqaggklcpnnlccsqwgfcglgsefcgggcqsg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~CG~~~~~~~C~~~~CCS~~G~CG~t~~~C~~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "1wkx_A") self.assertEqual( alignment.target.seq[1:40], "QCGRQAGGKLCPDNLCCSQWGWCGSTDEYCSPDHNCQSN" ) self.assertEqual(alignment.target.annotations["hmm_name"], "1wkx_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Hevein isoform 2; allergen, lectin, agglutinin-toxin motif; 1.70A {Hevea brasiliensis} PDB: 1hev_A 1q9b_A* 4wp4_A", ) self.assertEqual(alignment[0], "QCGRQAGGKLCPDNLCCSQWGWCGSTDEYCSPDHNCQSN") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSBGGGTTBCCSTTCEECTTSCEESSHHHHCGGGTCCBS ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCcCCCcccCCCCeEeecCcccCCcccccCCCCccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 47888888999999999999999999999996 89985 ", ) self.assertEqual( str(alignment), """\ 1wkx_A 1 QCGRQAGGKLCPDNLCCSQWGWCGSTDEYCSPDHNCQSN 40 0 .||.||||||||.||||||||.||...|.|..--.|||. 39 2UVO:A|PD 87 KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGG--GCQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 33, 35, 40], [ 87, 119, 119, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['Q', 'C', 'G', 'R', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'D', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'W', 'C', 'G', 'S', 'T', 'D', 'E', 'Y', 'C', 'S', 'P', 'D', 'H', 'N', 'C', 'Q', 'S', 'N'], ['K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', '-', '-', 'G', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 98.00) self.assertAlmostEqual(alignment.annotations["E-value"], 8e-09, places=10) self.assertAlmostEqual(alignment.annotations["Score"], 63.24) self.assertAlmostEqual(alignment.annotations["Identities"], 49) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.241) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 36.5) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:43], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTS" ) self.assertEqual(alignment[1], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTS") self.assertEqual( alignment.query.letter_annotations["Consensus"], " rcgeqgsnmecpnnlccsqygycgmggdycgkgcqngacwts ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~CG~~~~~~~C~~~~CCs~~G~CG~t~~~C~~gCq~~c~~~ ", ) self.assertEqual(alignment.target.id, "4mpi_A") self.assertEqual( alignment.target.seq[3:44], "QCGRQAGGALCPGGLCCSQYGWCANTPEYCGSGCQSQCDGG" ) self.assertEqual(alignment.target.annotations["hmm_name"], "4mpi_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Class I chitinase; hevein-like domain, chitin oligomers, sugar binding protein; HET: MES; 1.60A {Hevea brasiliensis subsp}", ) self.assertEqual(alignment[0], "QCGRQAGGALCPGGLCCSQYGWCANTPEYCGSGCQSQ-CDGG") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " BCBGGGTTBCCGGGCEECTTSBEECSHHHHSTTCCBCTTCC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ccCCcCCCcccCCCCcCcccceecCCcccccccccccCCCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 68888888999999999999999999999999999756543 ", ) self.assertEqual( str(alignment), """\ 4mpi_A 3 QCGRQAGGALCPGGLCCSQYGWCANTPEYCGSGCQSQ-CDGG 44 0 .||.|.....||..|||||||.|.....|||.|||..-|... 42 2UVO:A|PD 1 RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTS 43 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 3, 40, 40, 44], [ 1, 38, 39, 43]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['Q', 'C', 'G', 'R', 'Q', 'A', 'G', 'G', 'A', 'L', 'C', 'P', 'G', 'G', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'W', 'C', 'A', 'N', 'T', 'P', 'E', 'Y', 'C', 'G', 'S', 'G', 'C', 'Q', 'S', 'Q', '-', 'C', 'D', 'G', 'G'], ['R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.97) self.assertAlmostEqual(alignment.annotations["E-value"], 1e-08, places=9) self.assertAlmostEqual(alignment.annotations["Score"], 61.74) self.assertAlmostEqual(alignment.annotations["Identities"], 59) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.493) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 33.9) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[87:124], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG" ) self.assertEqual(alignment[1], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG-CQSG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " kcgsqaggklcpnnlccsqwgfcglgsefcgggcqsg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~CG~~~~~~~C~~~~CCS~~G~CG~t~~~C~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "2lb7_A") self.assertEqual( alignment.target.seq[2:40], "RCGDQARGAKCPNCLCCGKYGFCGSGDAYCGAGSCQSQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "2lb7_A") self.assertEqual( alignment.target.annotations["hmm_description"], "WAMP-1A, antimicrobial peptide 1A; antimicrobial protein; NMR {Triticum kiharae}", ) self.assertEqual(alignment[0], "RCGDQARGAKCPNCLCCGKYGFCGSGDAYCGAGSCQSQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " ECBGGGTTBCCCTTCEEETTTEEECSHHHHSTTSEEEC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCcCCCCCcccCCCCcCCcceeecCCccccCCCCccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 578888889999999999999999999999987 9976 ", ) self.assertEqual( str(alignment), """\ 2lb7_A 2 RCGDQARGAKCPNCLCCGKYGFCGSGDAYCGAGSCQSQ 40 0 .||.||.|..|||.|||...||||.|...||.|-|||. 38 2UVO:A|PD 87 KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG-CQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 35, 36, 40], [ 87, 120, 120, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'C', 'G', 'D', 'Q', 'A', 'R', 'G', 'A', 'K', 'C', 'P', 'N', 'C', 'L', 'C', 'C', 'G', 'K', 'Y', 'G', 'F', 'C', 'G', 'S', 'G', 'D', 'A', 'Y', 'C', 'G', 'A', 'G', 'S', 'C', 'Q', 'S', 'Q'], ['K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', '-', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.88) self.assertAlmostEqual(alignment.annotations["E-value"], 2e-08, places=9) self.assertAlmostEqual(alignment.annotations["Score"], 62.00) self.assertAlmostEqual(alignment.annotations["Identities"], 49) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.238) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 33.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:38], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNG" ) self.assertEqual(alignment[1], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKG-CQNG") self.assertEqual( alignment.query.letter_annotations["Consensus"], "ercgeqgsnmecpnnlccsqygycgmggdycgkgcqng ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~~CG~~~~~~C~~~~CCS~~G~CG~t~~~C~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "1p9g_A") self.assertEqual( alignment.target.seq[0:38], "ETCASRCPRPCNAGLCCSIYGYCGSGAAYCGAGNCRCQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "1p9g_A") self.assertEqual( alignment.target.annotations["hmm_description"], "EAFP 2; antifungal peptide, atomic resolution, antifungal protein; HET: PCA; 0.84A {Eucommia ulmoides} SCOP: g.3.1.1 PDB: 1p9z_A*", ) self.assertEqual(alignment[0], "ETCA-SRCPRPCNAGLCCSIYGYCGSGAAYCGAGNCRCQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CCGGGGTTCCSCTTCEEETTSCEECSHHHHSTTTEEEC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCcCCcCCcccCCCCeECccceeCCCccccCCCccccC ", ) self.assertEqual( alignment.column_annotations["Confidence"], "689957888999999999999999999999995 9976 ", ) self.assertEqual( str(alignment), """\ 1p9g_A 0 ETCA-SRCPRPCNAGLCCSIYGYCGSGAAYCGAGNCRCQ 38 0 |.|.-......|...||||.|||||.|..|||.|-|... 39 2UVO:A|PD 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKG-CQNG 38 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 4, 4, 33, 34, 38], [ 0, 4, 5, 34, 34, 38]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'T', 'C', 'A', '-', 'S', 'R', 'C', 'P', 'R', 'P', 'C', 'N', 'A', 'G', 'L', 'C', 'C', 'S', 'I', 'Y', 'G', 'Y', 'C', 'G', 'S', 'G', 'A', 'A', 'Y', 'C', 'G', 'A', 'G', 'N', 'C', 'R', 'C', 'Q'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', '-', 'C', 'Q', 'N', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.83) self.assertAlmostEqual(alignment.annotations["E-value"], 2.8e-08, places=9) self.assertAlmostEqual(alignment.annotations["Score"], 58.62) self.assertAlmostEqual(alignment.annotations["Identities"], 44) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.336) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 25.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual(alignment.query.seq[91:118], "QAGGKLCPNNLCCSQWGFCGLGSEFCG") self.assertEqual(alignment[1], "QAGGKLCPNNLCCSQWGFCGLGSEFCG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " qaggklcpnnlccsqwgfcglgsefcg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~C~~~~CCS~~G~CG~t~~~C~ ", ) self.assertEqual(alignment.target.id, "1mmc_A") self.assertEqual(alignment.target.seq[2:29], "ECVRGRCPSGMCCSQFGYCGKGPKYCG") self.assertEqual(alignment.target.annotations["hmm_name"], "1mmc_A") self.assertEqual( alignment.target.annotations["hmm_description"], "AC-AMP2, antimicrobial peptide 2; antifungal antimicrobial, chitin-binding; NMR {Amaranthus caudatus} SCOP: g.3.1.2 PDB: 1zuv_A 1zwu_A* 1znt_A*", ) self.assertEqual(alignment[0], "ECVRGRCPSGMCCSQFGYCGKGPKYCG") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCSSSCCSTTCEECTTSCEESSHHHHC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCccCCCCCCCcccccceeCCchHhhC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 788889999999999999999999996 ", ) self.assertEqual( str(alignment), """\ 1mmc_A 2 ECVRGRCPSGMCCSQFGYCGKGPKYCG 29 0 ......||...||||.|.||.|...|| 27 2UVO:A|PD 91 QAGGKLCPNNLCCSQWGFCGLGSEFCG 118 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 29], [ 91, 118]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'C', 'V', 'R', 'G', 'R', 'C', 'P', 'S', 'G', 'M', 'C', 'C', 'S', 'Q', 'F', 'G', 'Y', 'C', 'G', 'K', 'G', 'P', 'K', 'Y', 'C', 'G'], ['Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.83) self.assertAlmostEqual(alignment.annotations["E-value"], 2.9e-08, places=9) self.assertAlmostEqual(alignment.annotations["Score"], 61.32) self.assertAlmostEqual(alignment.annotations["Identities"], 39) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.187) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 32.1) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[87:124], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG" ) self.assertEqual(alignment[1], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG-CQSG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " kcgsqaggklcpnnlccsqwgfcglgsefcgggcqsg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~CG~~~~~~C~~~~CCS~~G~CG~t~~~C~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "1p9g_A") self.assertEqual( alignment.target.seq[1:38], "TCASRCPRPCNAGLCCSIYGYCGSGAAYCGAGNCRCQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "1p9g_A") self.assertEqual( alignment.target.annotations["hmm_description"], "EAFP 2; antifungal peptide, atomic resolution, antifungal protein; HET: PCA; 0.84A {Eucommia ulmoides} SCOP: g.3.1.1 PDB: 1p9z_A*", ) self.assertEqual(alignment[0], "TCA-SRCPRPCNAGLCCSIYGYCGSGAAYCGAGNCRCQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CGGGGTTCCSCTTCEEETTSCEECSHHHHSTTTEEEC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CcCCcCCcccCCCCeECccceeCCCccccCCCccccC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 47747788999999999999999999999985 9986 ", ) self.assertEqual( str(alignment), """\ 1p9g_A 1 TCA-SRCPRPCNAGLCCSIYGYCGSGAAYCGAGNCRCQ 38 0 .|.-......|...||||..|.||.|...||.|-|... 38 2UVO:A|PD 87 KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGG-CQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 4, 4, 33, 34, 38], [ 87, 90, 91, 120, 120, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'C', 'A', '-', 'S', 'R', 'C', 'P', 'R', 'P', 'C', 'N', 'A', 'G', 'L', 'C', 'C', 'S', 'I', 'Y', 'G', 'Y', 'C', 'G', 'S', 'G', 'A', 'A', 'Y', 'C', 'G', 'A', 'G', 'N', 'C', 'R', 'C', 'Q'], ['K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', '-', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.76) self.assertAlmostEqual(alignment.annotations["E-value"], 4.7e-08, places=9) self.assertAlmostEqual(alignment.annotations["Score"], 59.52) self.assertAlmostEqual(alignment.annotations["Identities"], 50) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.302) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 34.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:38], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNG" ) self.assertEqual(alignment[1], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGK--GCQNG") self.assertEqual( alignment.query.letter_annotations["Consensus"], "ercgeqgsnmecpnnlccsqygycgmggdycgkgcqng ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~~CG~~~~~~~C~~~~CCS~~G~CG~t~~~C~~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "1wkx_A") self.assertEqual( alignment.target.seq[0:40], "EQCGRQAGGKLCPDNLCCSQWGWCGSTDEYCSPDHNCQSN" ) self.assertEqual(alignment.target.annotations["hmm_name"], "1wkx_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Hevein isoform 2; allergen, lectin, agglutinin-toxin motif; 1.70A {Hevea brasiliensis} PDB: 1hev_A 1q9b_A* 4wp4_A", ) self.assertEqual(alignment[0], "EQCGRQAGGKLCPDNLCCSQWGWCGSTDEYCSPDHNCQSN") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CCSBGGGTTBCCSTTCEECTTSCEESSHHHHCGGGTCCBS ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCCCCcCCCcccCCCCeEeecCcccCCcccccCCCCccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], "589999888999999999999999999999997 78864 ", ) self.assertEqual( str(alignment), """\ 1wkx_A 0 EQCGRQAGGKLCPDNLCCSQWGWCGSTDEYCSPDHNCQSN 40 0 |.||.|.....||.||||||.|.||....||..--.||.. 40 2UVO:A|PD 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGK--GCQNG 38 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 33, 35, 40], [ 0, 33, 33, 38]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'Q', 'C', 'G', 'R', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'D', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'W', 'C', 'G', 'S', 'T', 'D', 'E', 'Y', 'C', 'S', 'P', 'D', 'H', 'N', 'C', 'Q', 'S', 'N'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', '-', '-', 'G', 'C', 'Q', 'N', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.58) self.assertAlmostEqual(alignment.annotations["E-value"], 1.5e-07, places=8) self.assertAlmostEqual(alignment.annotations["Score"], 56.59) self.assertAlmostEqual(alignment.annotations["Identities"], 55) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.488) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 34.3) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:38], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNG" ) self.assertEqual(alignment[1], "ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKG-CQNG") self.assertEqual( alignment.query.letter_annotations["Consensus"], "ercgeqgsnmecpnnlccsqygycgmggdycgkgcqng ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~CG~~~~~~~C~~~~CCS~~G~CG~t~~~C~~~~Cq~~ ", ) self.assertEqual(alignment.target.id, "2lb7_A") self.assertEqual( alignment.target.seq[1:40], "QRCGDQARGAKCPNCLCCGKYGFCGSGDAYCGAGSCQSQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "2lb7_A") self.assertEqual( alignment.target.annotations["hmm_description"], "WAMP-1A, antimicrobial peptide 1A; antimicrobial protein; NMR {Triticum kiharae}", ) self.assertEqual(alignment[0], "QRCGDQARGAKCPNCLCCGKYGFCGSGDAYCGAGSCQSQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " EECBGGGTTBCCCTTCEEETTTEEECSHHHHSTTSEEEC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCcCCCCCcccCCCCcCCcceeecCCccccCCCCccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 4788888888999999999999999999999987 8865 ", ) self.assertEqual( str(alignment), """\ 2lb7_A 1 QRCGDQARGAKCPNCLCCGKYGFCGSGDAYCGAGSCQSQ 40 0 .|||.|.....|||.|||..||.||.|..|||.|-||.. 39 2UVO:A|PD 0 ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKG-CQNG 38 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 35, 36, 40], [ 0, 34, 34, 38]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['Q', 'R', 'C', 'G', 'D', 'Q', 'A', 'R', 'G', 'A', 'K', 'C', 'P', 'N', 'C', 'L', 'C', 'C', 'G', 'K', 'Y', 'G', 'F', 'C', 'G', 'S', 'G', 'D', 'A', 'Y', 'C', 'G', 'A', 'G', 'S', 'C', 'Q', 'S', 'Q'], ['E', 'R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', '-', 'C', 'Q', 'N', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.58) self.assertAlmostEqual(alignment.annotations["E-value"], 1.6e-07, places=8) self.assertAlmostEqual(alignment.annotations["Score"], 55.11) self.assertAlmostEqual(alignment.annotations["Identities"], 42) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.250) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 23.2) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual(alignment.query.seq[92:118], "AGGKLCPNNLCCSQWGFCGLGSEFCG") self.assertEqual(alignment[1], "AGGKLCPNNLCCSQWGFCGLGSEFCG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " aggklcpnnlccsqwgfcglgsefcg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " cg~~~C~~~~CCs~~G~CGtt~~~C~", ) self.assertEqual(alignment.target.id, "2n1s_A") self.assertEqual(alignment.target.seq[4:30], "CYRGRCSGGLCCSKYGYCGSGPAYCG") self.assertEqual(alignment.target.annotations["hmm_name"], "2n1s_A") self.assertEqual( alignment.target.annotations["hmm_description"], "AMP-2; antimicrobial peptide, ICK, cystine knot inhibitor, cystine antimicrobial protein; NMR {Stellaria media}", ) self.assertEqual(alignment[0], "CYRGRCSGGLCCSKYGYCGSGPAYCG") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CBTTBCSTTCEECTTSBEECSHHHHC", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCCCCCCCCCccccccccCcchhhcC", ) self.assertEqual( alignment.column_annotations["Confidence"], " 34568999999999999999999985", ) self.assertEqual( str(alignment), """\ 2n1s_A 4 CYRGRCSGGLCCSKYGYCGSGPAYCG 30 0 .....|...||||..|.||.|...|| 26 2UVO:A|PD 92 AGGKLCPNNLCCSQWGFCGLGSEFCG 118 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 4, 30], [ 92, 118]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'Y', 'R', 'G', 'R', 'C', 'S', 'G', 'G', 'L', 'C', 'C', 'S', 'K', 'Y', 'G', 'Y', 'C', 'G', 'S', 'G', 'P', 'A', 'Y', 'C', 'G'], ['A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.56) self.assertAlmostEqual(alignment.annotations["E-value"], 1.7e-07, places=8) self.assertAlmostEqual(alignment.annotations["Score"], 55.43) self.assertAlmostEqual(alignment.annotations["Identities"], 42) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.160) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 29.5) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[83:118], "RADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCG" ) self.assertEqual(alignment[1], "RADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " radikcgsqaggklcpnnlccsqwgfcglgsefcg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~CG~~~g~C~~g~CCS~~G~CG~~~~~C~ ", ) self.assertEqual(alignment.target.id, "2kus_A") self.assertEqual( alignment.target.seq[1:34], "GPNGQCGPGWGGCRGGLCCSQYGYCGSGPKYCA" ) self.assertEqual(alignment.target.annotations["hmm_name"], "2kus_A") self.assertEqual( alignment.target.annotations["hmm_description"], "SM-AMP-1.1A; plant antimicrobial peptide, chitin-binding peptide, antimic protein; NMR {Stellaria media}", ) self.assertEqual(alignment[0], "GPNGQCGPGWG--GCRGGLCCSQYGYCGSGPKYCA") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CTTCBCBTTTBCCCTTCEECTTSBEECSHHHHC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCcccCCCCCcCCCCcEECCCceecCChhhhC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 467889988876999999999999999999986 ", ) self.assertEqual( str(alignment), """\ 2kus_A 1 GPNGQCGPGWG--GCRGGLCCSQYGYCGSGPKYCA 34 0 .....||...|--.|...|||||.|.||.|...|. 35 2UVO:A|PD 83 RADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCG 118 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 12, 12, 34], [ 83, 94, 96, 118]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'P', 'N', 'G', 'Q', 'C', 'G', 'P', 'G', 'W', 'G', '-', '-', 'G', 'C', 'R', 'G', 'G', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'S', 'G', 'P', 'K', 'Y', 'C', 'A'], ['R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.24) self.assertAlmostEqual(alignment.annotations["E-value"], 1.1e-06) self.assertAlmostEqual(alignment.annotations["Score"], 69.81) self.assertAlmostEqual(alignment.annotations["Identities"], 68) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.622) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 35.1) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[87:124], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG" ) self.assertEqual(alignment[1], "KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " kcgsqaggklcpnnlccsqwgfcglgsefcgggcqsg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~cG~~~~~~~c~~~~ccs~~g~cg~~~~~C~~~cq~~ ", ) self.assertEqual(alignment.target.id, "2dkv_A") self.assertEqual( alignment.target.seq[2:39], "QCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "2dkv_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Chitinase; whole structure, oryza sativa L. japonica, hydrolase; HET: MES; 2.00A {Oryza sativa japonica group} PDB: 3iwr_A*", ) self.assertEqual(alignment[0], "QCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " BCSTTTTTCCCGGGCEECTTSBEESSHHHHSTTCCBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCcCCCCCeeCcCCcccCCccccCccccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 4888889999999999999999999999999999987 ", ) self.assertEqual( str(alignment), """\ 2dkv_A 2 QCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQ 39 0 .||.||||..|||.||||.||.||..|.|||.||||. 37 2UVO:A|PD 87 KCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSG 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 39], [ 87, 124]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['Q', 'C', 'G', 'A', 'Q', 'A', 'G', 'G', 'A', 'R', 'C', 'P', 'N', 'C', 'L', 'C', 'C', 'S', 'R', 'W', 'G', 'W', 'C', 'G', 'T', 'T', 'S', 'D', 'F', 'C', 'G', 'D', 'G', 'C', 'Q', 'S', 'Q'], ['K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.14) self.assertAlmostEqual(alignment.annotations["E-value"], 1.9e-06) self.assertAlmostEqual(alignment.annotations["Score"], 50.76) self.assertAlmostEqual(alignment.annotations["Identities"], 50) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.394) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 24.5) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual(alignment.query.seq[5:33], "QGSNMECPNNLCCSQYGYCGMGGDYCGK") self.assertEqual(alignment[1], "QGSNMECPNNLCCSQYGYCGMGGDYCGK") self.assertEqual( alignment.query.letter_annotations["Consensus"], " qgsnmecpnnlccsqygycgmggdycgk ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~C~~~~CCS~~G~CG~t~~~C~~", ) self.assertEqual(alignment.target.id, "1mmc_A") self.assertEqual(alignment.target.seq[2:30], "ECVRGRCPSGMCCSQFGYCGKGPKYCGR") self.assertEqual(alignment.target.annotations["hmm_name"], "1mmc_A") self.assertEqual( alignment.target.annotations["hmm_description"], "AC-AMP2, antimicrobial peptide 2; antifungal antimicrobial, chitin-binding; NMR {Amaranthus caudatus} SCOP: g.3.1.2 PDB: 1zuv_A 1zwu_A* 1znt_A*", ) self.assertEqual(alignment[0], "ECVRGRCPSGMCCSQFGYCGKGPKYCGR") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCSSSCCSTTCEECTTSCEESSHHHHCC", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCccCCCCCCCcccccceeCCchHhhCc", ) self.assertEqual( alignment.column_annotations["Confidence"], " 4456689999999999999999999974", ) self.assertEqual( str(alignment), """\ 1mmc_A 2 ECVRGRCPSGMCCSQFGYCGKGPKYCGR 30 0 ......||...||||.||||.|..|||. 28 2UVO:A|PD 5 QGSNMECPNNLCCSQYGYCGMGGDYCGK 33 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 30], [ 5, 33]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'C', 'V', 'R', 'G', 'R', 'C', 'P', 'S', 'G', 'M', 'C', 'C', 'S', 'Q', 'F', 'G', 'Y', 'C', 'G', 'K', 'G', 'P', 'K', 'Y', 'C', 'G', 'R'], ['Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 97.02) self.assertAlmostEqual(alignment.annotations["E-value"], 3.5e-06) self.assertAlmostEqual(alignment.annotations["Score"], 49.35) self.assertAlmostEqual(alignment.annotations["Identities"], 56) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.468) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 23.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual(alignment.query.seq[1:32], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCG") self.assertEqual(alignment[1], "RCGEQGSNMECPNNLCCSQYGYCGMGGDYCG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " rcgeqgsnmecpnnlccsqygycgmggdycg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~cg~~~C~~~~CCs~~G~CGtt~~~C~", ) self.assertEqual(alignment.target.id, "2n1s_A") self.assertEqual(alignment.target.seq[3:30], "QCYRGRCSGGLCCSKYGYCGSGPAYCG") self.assertEqual(alignment.target.annotations["hmm_name"], "2n1s_A") self.assertEqual( alignment.target.annotations["hmm_description"], "AMP-2; antimicrobial peptide, ICK, cystine knot inhibitor, cystine antimicrobial protein; NMR {Stellaria media}", ) self.assertEqual(alignment[0], "QCY----RGRCSGGLCCSKYGYCGSGPAYCG") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " BCBTTBCSTTCEECTTSBEECSHHHHC", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " hcCCCCCCCCCccccccccCcchhhcC", ) self.assertEqual( alignment.column_annotations["Confidence"], " 566348999999999999999999985", ) self.assertEqual( str(alignment), """\ 2n1s_A 3 QCY----RGRCSGGLCCSKYGYCGSGPAYCG 30 0 .|.----...|...||||.|||||.|..||| 31 2UVO:A|PD 1 RCGEQGSNMECPNNLCCSQYGYCGMGGDYCG 32 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 3, 6, 6, 30], [ 1, 4, 8, 32]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['Q', 'C', 'Y', '-', '-', '-', '-', 'R', 'G', 'R', 'C', 'S', 'G', 'G', 'L', 'C', 'C', 'S', 'K', 'Y', 'G', 'Y', 'C', 'G', 'S', 'G', 'P', 'A', 'Y', 'C', 'G'], ['R', 'C', 'G', 'E', 'Q', 'G', 'S', 'N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 96.79) self.assertAlmostEqual(alignment.annotations["E-value"], 9.9e-06) self.assertAlmostEqual(alignment.annotations["Score"], 64.37) self.assertAlmostEqual(alignment.annotations["Identities"], 53) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.380) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 35.8) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[43:81], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGG" ) self.assertEqual(alignment[1], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " krcgsqaggatctnnqccsqygycgfgaeycgagcqgg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~cG~~~~~~~c~~~~ccs~~g~cg~~~~~C~~~cq~~ ", ) self.assertEqual(alignment.target.id, "2dkv_A") self.assertEqual( alignment.target.seq[1:39], "EQCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQ" ) self.assertEqual(alignment.target.annotations["hmm_name"], "2dkv_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Chitinase; whole structure, oryza sativa L. japonica, hydrolase; HET: MES; 2.00A {Oryza sativa japonica group} PDB: 3iwr_A*", ) self.assertEqual(alignment[0], "EQCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQ") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CBCSTTTTTCCCGGGCEECTTSBEESSHHHHSTTCCBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCcCCCCCeeCcCCcccCCccccCccccCC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 47999999999999999999999999999999999965 ", ) self.assertEqual( str(alignment), """\ 2dkv_A 1 EQCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQ 39 0 ..||.|||||.|.|..|||..|.||.....||.|||.. 38 2UVO:A|PD 43 KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGG 81 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 39], [43, 81]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'Q', 'C', 'G', 'A', 'Q', 'A', 'G', 'G', 'A', 'R', 'C', 'P', 'N', 'C', 'L', 'C', 'C', 'S', 'R', 'W', 'G', 'W', 'C', 'G', 'T', 'T', 'S', 'D', 'F', 'C', 'G', 'D', 'G', 'C', 'Q', 'S', 'Q'], ['K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 96.68) self.assertAlmostEqual(alignment.annotations["E-value"], 1.6e-05) self.assertAlmostEqual(alignment.annotations["Score"], 46.90) self.assertAlmostEqual(alignment.annotations["Identities"], 50) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.287) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 28.1) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[42:76], "SKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGA" ) self.assertEqual(alignment[1], "SKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGA") self.assertEqual( alignment.query.letter_annotations["Consensus"], " skrcgsqaggatctnnqccsqygycgfgaeycga ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~CG~~~g~C~~g~CCS~~G~CG~~~~~C~~", ) self.assertEqual(alignment.target.id, "2kus_A") self.assertEqual(alignment.target.seq[3:35], "NGQCGPGWGGCRGGLCCSQYGYCGSGPKYCAH") self.assertEqual(alignment.target.annotations["hmm_name"], "2kus_A") self.assertEqual( alignment.target.annotations["hmm_description"], "SM-AMP-1.1A; plant antimicrobial peptide, chitin-binding peptide, antimic protein; NMR {Stellaria media}", ) self.assertEqual(alignment[0], "NGQCGPGWG--GCRGGLCCSQYGYCGSGPKYCAH") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " TCBCBTTTBCCCTTCEECTTSBEECSHHHHCC", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CcccCCCCCcCCCCcEECCCceecCChhhhCc", ) self.assertEqual( alignment.column_annotations["Confidence"], " 45788888779999999999999999999963", ) self.assertEqual( str(alignment), """\ 2kus_A 3 NGQCGPGWG--GCRGGLCCSQYGYCGSGPKYCAH 35 0 ...||...|--.|....|||||||||.|..||.. 34 2UVO:A|PD 42 SKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGA 76 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 3, 12, 12, 35], [42, 51, 53, 76]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['N', 'G', 'Q', 'C', 'G', 'P', 'G', 'W', 'G', '-', '-', 'G', 'C', 'R', 'G', 'G', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'S', 'G', 'P', 'K', 'Y', 'C', 'A', 'H'], ['S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 92.12) self.assertAlmostEqual(alignment.annotations["E-value"], 0.024) self.assertAlmostEqual(alignment.annotations["Score"], 45.43) self.assertAlmostEqual(alignment.annotations["Identities"], 20) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.652) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 136.2) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[8:169], "NMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC", ) self.assertEqual( alignment[1], "NMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " nmecpnnlccsqygycgmggdycgkgcqngacwtskrcgsqaggatctnnqccsqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgacstdkpcgkdaggrvctnnyccskwgscgigpgycgagcqsggc ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~c~~~~cc~~~~~c~~~~~~c~~~c~~~~c~~~~~c~~~~~~c~~~~cc~~~~~c~~~~~~c~~~c~~~~c~~~~~c~~~~~~c~~~~cc~~~~~c~~~~~~c~~~c~~~~c~~~~~c~~~~~~c~~~~cc~~~~~c~~~~~~c~~~c~~~~c ", ) self.assertEqual(alignment.target.id, "1wga") self.assertEqual( alignment.target.seq[8:163], "XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXXXXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXXXXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXXXXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXC", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1wga") self.assertEqual( alignment.target.annotations["hmm_description"], "; lectin (agglutinin); NMR {}", ) self.assertEqual( alignment[0], "XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXC", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 45688889999999999999999999999999999988754467999999999999999999999999999999999887544679999999999999999999999999999999998876446799999999999998888888877765444 ", ) self.assertEqual( str(alignment), """\ 1wga 8 XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCX 0 ...|....||.....|......|...|....|.....|...--...|....||.....|. 2UVO:A|PD 8 NMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCG 1wga 66 XXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXX 60 .....|...|....|.....|...--...|....||.....|......|...|....|.. 2UVO:A|PD 68 FGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACST 1wga 124 XXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXC 163 120 ...|...--...|....||.....|......|...|....| 161 2UVO:A|PD 128 DKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC 169 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 8, 49, 49, 90, 90, 131, 131, 163], [ 8, 49, 51, 92, 94, 135, 137, 169]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', '-', '-', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', '-', '-', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', '-', '-', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C'], ['N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C', 'S', 'T', 'D', 'K', 'P', 'C', 'G', 'K', 'D', 'A', 'G', 'G', 'R', 'V', 'C', 'T', 'N', 'N', 'Y', 'C', 'C', 'S', 'K', 'W', 'G', 'S', 'C', 'G', 'I', 'G', 'P', 'G', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'S', 'G', 'G', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 88.54) self.assertAlmostEqual(alignment.annotations["E-value"], 0.1) self.assertAlmostEqual(alignment.annotations["Score"], 39.32) self.assertAlmostEqual(alignment.annotations["Identities"], 37) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.037) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 27.7) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[83:118], "RADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCG" ) self.assertEqual(alignment[1], "RADIKCGSQA-----GGKLCPN---NLCCSQWGFCGLGSEFCG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " radikcgsqaggklcpnnlccsqwgfcglgsefcg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " r~d~rCg~~~~~~~~~~~~C~~~~~~~CCs~~~~cg~~~~~c~ ", ) self.assertEqual(alignment.target.id, "4z8i_A") self.assertEqual( alignment.target.seq[5:48], "RSDGRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCT" ) self.assertEqual(alignment.target.annotations["hmm_name"], "4z8i_A") self.assertEqual( alignment.target.annotations["hmm_description"], "BBTPGRP3, peptidoglycan recognition protein 3; chitin-binding domain, AM hydrolase; 2.70A {Branchiostoma belcheri tsingtauense}", ) self.assertEqual(alignment[0], "RSDGRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCT") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSSSBCBSSSCBTTBSSBBCCTTSSCCEECTTSBEECSHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCEEeCCccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 5566677665 5567775 899999999999999886 ", ) self.assertEqual( str(alignment), """\ 4z8i_A 5 RSDGRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCT 48 0 |.|..||...-----....|..---..|||.||.||.....|. 43 2UVO:A|PD 83 RADIKCGSQA-----GGKLCPN---NLCCSQWGFCGLGSEFCG 118 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 5, 15, 20, 27, 30, 48], [ 83, 93, 93, 100, 100, 118]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'S', 'D', 'G', 'R', 'C', 'G', 'P', 'N', 'Y', 'P', 'A', 'P', 'D', 'A', 'N', 'P', 'G', 'E', 'C', 'N', 'P', 'H', 'A', 'V', 'D', 'H', 'C', 'C', 'S', 'E', 'W', 'G', 'W', 'C', 'G', 'R', 'E', 'T', 'S', 'H', 'C', 'T'], ['R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', '-', '-', '-', '-', '-', 'G', 'G', 'K', 'L', 'C', 'P', 'N', '-', '-', '-', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 88.13) self.assertAlmostEqual(alignment.annotations["E-value"], 0.12) self.assertAlmostEqual(alignment.annotations["Score"], 39.05) self.assertAlmostEqual(alignment.annotations["Identities"], 33) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.005) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 26.8) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[42:75], "SKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCG" ) self.assertEqual(alignment[1], "SKRCGSQA-----GGATCTN---NQCCSQYGYCGFGAEYCG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " skrcgsqaggatctnnqccsqygycgfgaeycg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " d~rCg~~~~~~~~~~~~C~~~~~~~CCs~~~~cg~~~~~c~ ", ) self.assertEqual(alignment.target.id, "4z8i_A") self.assertEqual( alignment.target.seq[7:48], "DGRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCT" ) self.assertEqual(alignment.target.annotations["hmm_name"], "4z8i_A") self.assertEqual( alignment.target.annotations["hmm_description"], "BBTPGRP3, peptidoglycan recognition protein 3; chitin-binding domain, AM hydrolase; 2.70A {Branchiostoma belcheri tsingtauense}", ) self.assertEqual(alignment[0], "DGRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCT") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " SSBCBSSSCBTTBSSBBCCTTSSCCEECTTSBEECSHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCCCCCCcccCCCCCCCCCCCCCEEeCCccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 34666665 6678875 899999999999999997 ", ) self.assertEqual( str(alignment), """\ 4z8i_A 7 DGRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCT 48 0 ..|||...-----....|..---..|||..|.||.....|. 41 2UVO:A|PD 42 SKRCGSQA-----GGATCTN---NQCCSQYGYCGFGAEYCG 75 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 7, 15, 20, 27, 30, 48], [42, 50, 50, 57, 57, 75]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['D', 'G', 'R', 'C', 'G', 'P', 'N', 'Y', 'P', 'A', 'P', 'D', 'A', 'N', 'P', 'G', 'E', 'C', 'N', 'P', 'H', 'A', 'V', 'D', 'H', 'C', 'C', 'S', 'E', 'W', 'G', 'W', 'C', 'G', 'R', 'E', 'T', 'S', 'H', 'C', 'T'], ['S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', '-', '-', '-', '-', '-', 'G', 'G', 'A', 'T', 'C', 'T', 'N', '-', '-', '-', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 85.66) self.assertAlmostEqual(alignment.annotations["E-value"], 0.21) self.assertAlmostEqual(alignment.annotations["Score"], 38.06) self.assertAlmostEqual(alignment.annotations["Identities"], 37) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.037) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[83:118], "RADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCG" ) self.assertEqual(alignment[1], "RADIKCGSQA-----GGKLCPN---NLCCSQWGFCGLGSEFCG") self.assertEqual( alignment.query.letter_annotations["Consensus"], " radikcgsqaggklcpnnlccsqwgfcglgsefcg ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~d~~Cg~~~~~~~~~~~~C~~~~~~~CCs~~~~Cg~~~~~C~ ", ) self.assertEqual(alignment.target.id, "4zxm_A") self.assertEqual( alignment.target.seq[22:65], "RSDGRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCT" ) self.assertEqual(alignment.target.annotations["hmm_name"], "4zxm_A") self.assertEqual( alignment.target.annotations["hmm_description"], "PGRP domain of peptidoglycan recognition protein; amidase, hydrolase; 2.80A {Branchiostoma belcheri tsingtauense}", ) self.assertEqual(alignment[0], "RSDGRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCT") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCeEeCCCCCcC ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 3455555554 4457776 899999999999999875 ", ) self.assertEqual( str(alignment), """\ 4zxm_A 22 RSDGRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCT 65 0 |.|..||...-----....|..---..|||.||.||.....|. 43 2UVO:A|PD 83 RADIKCGSQA-----GGKLCPN---NLCCSQWGFCGLGSEFCG 118 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 22, 32, 37, 44, 47, 65], [ 83, 93, 93, 100, 100, 118]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'S', 'D', 'G', 'R', 'C', 'G', 'P', 'N', 'Y', 'P', 'A', 'P', 'D', 'A', 'N', 'P', 'G', 'E', 'C', 'N', 'P', 'H', 'A', 'V', 'D', 'H', 'C', 'C', 'S', 'E', 'W', 'G', 'W', 'C', 'G', 'R', 'E', 'T', 'S', 'H', 'C', 'T'], ['R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', '-', '-', '-', '-', '-', 'G', 'G', 'K', 'L', 'C', 'P', 'N', '-', '-', '-', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 85.31) self.assertAlmostEqual(alignment.annotations["E-value"], 0.23) self.assertAlmostEqual(alignment.annotations["Score"], 37.89) self.assertAlmostEqual(alignment.annotations["Identities"], 33) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.023) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[43:79], "KRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQ" ) self.assertEqual(alignment[1], "KRCGSQA-----GGATCTN---NQCCSQYGYCGFGAEYCG-AGCQ") self.assertEqual( alignment.query.letter_annotations["Consensus"], " krcgsqaggatctnnqccsqygycgfgaeycgagcq ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~Cg~~~~~~~~~~~~C~~~~~~~CCs~~~~Cg~~~~~C~~~~c~ ", ) self.assertEqual(alignment.target.id, "4zxm_A") self.assertEqual( alignment.target.seq[25:70], "GRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCTCSSCV" ) self.assertEqual(alignment.target.annotations["hmm_name"], "4zxm_A") self.assertEqual( alignment.target.annotations["hmm_description"], "PGRP domain of peptidoglycan recognition protein; amidase, hydrolase; 2.80A {Branchiostoma belcheri tsingtauense}", ) self.assertEqual(alignment[0], "GRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCTCSSCV") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCCCCCcccCCCCCCCCCCCCCeEeCCCCCcCCcccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 4566655 5578876 899999999999999986 4555 ", ) self.assertEqual( str(alignment), """\ 4zxm_A 25 GRCGPNYPAPDANPGECNPHAVDHCCSEWGWCGRETSHCTCSSCV 70 0 .|||...-----....|..---..|||..|.||.....|.-..|. 45 2UVO:A|PD 43 KRCGSQA-----GGATCTN---NQCCSQYGYCGFGAEYCG-AGCQ 79 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[25, 32, 37, 44, 47, 65, 66, 70], [43, 50, 50, 57, 57, 75, 75, 79]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'R', 'C', 'G', 'P', 'N', 'Y', 'P', 'A', 'P', 'D', 'A', 'N', 'P', 'G', 'E', 'C', 'N', 'P', 'H', 'A', 'V', 'D', 'H', 'C', 'C', 'S', 'E', 'W', 'G', 'W', 'C', 'G', 'R', 'E', 'T', 'S', 'H', 'C', 'T', 'C', 'S', 'S', 'C', 'V'], ['K', 'R', 'C', 'G', 'S', 'Q', 'A', '-', '-', '-', '-', '-', 'G', 'G', 'A', 'T', 'C', 'T', 'N', '-', '-', '-', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', '-', 'A', 'G', 'C', 'Q']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 72.00) self.assertAlmostEqual(alignment.annotations["E-value"], 1.3) self.assertAlmostEqual(alignment.annotations["Score"], 35.47) self.assertAlmostEqual(alignment.annotations["Identities"], 20) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.657) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 98.0) self.assertEqual(alignment.query.id, "2UVO:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[8:126], "NMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGAC", ) self.assertEqual( alignment[1], "NMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGAC", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " nmecpnnlccsqygycgmggdycgkgcqngacwtskrcgsqaggatctnnqccsqygycgfgaeycgagcqggpcradikcgsqaggklcpnnlccsqwgfcglgsefcgggcqsgac ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~c~~~~cc~~~~~c~~~~~~c~~~c~~~~c~~~~~c~~~~~~c~~~~cc~~~~~c~~~~~~c~~~c~~~~c~~~~~c~~~~~~c~~~~cc~~~~~c~~~~~~c~~~c~~~~c ", ) self.assertEqual(alignment.target.id, "1wga") self.assertEqual( alignment.target.seq[49:163], "XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXXXXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXXXXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXC", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1wga") self.assertEqual( alignment.target.annotations["hmm_description"], "; lectin (agglutinin); NMR {}", ) self.assertEqual( alignment[0], "XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXC", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 456788899999999999999999999999999998887544679999999999999999999999999999999998875446799999999999998888888776655443 ", ) self.assertEqual( str(alignment), """\ 1wga 49 XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCX 0 ...|....||.....|......|...|....|.....|...--...|....||.....|. 2UVO:A|PD 8 NMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCG 1wga 107 XXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXC 60 .....|...|....|.....|...--...|....||.....|......|...|....| 2UVO:A|PD 68 FGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGAC 1wga 163 118 2UVO:A|PD 126 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 49, 90, 90, 131, 131, 163], [ 8, 49, 51, 92, 94, 126]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', '-', '-', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', '-', '-', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C', 'C', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'C', 'X', 'X', 'X', 'X', 'C'], ['N', 'M', 'E', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'M', 'G', 'G', 'D', 'Y', 'C', 'G', 'K', 'G', 'C', 'Q', 'N', 'G', 'A', 'C', 'W', 'T', 'S', 'K', 'R', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'A', 'T', 'C', 'T', 'N', 'N', 'Q', 'C', 'C', 'S', 'Q', 'Y', 'G', 'Y', 'C', 'G', 'F', 'G', 'A', 'E', 'Y', 'C', 'G', 'A', 'G', 'C', 'Q', 'G', 'G', 'P', 'C', 'R', 'A', 'D', 'I', 'K', 'C', 'G', 'S', 'Q', 'A', 'G', 'G', 'K', 'L', 'C', 'P', 'N', 'N', 'L', 'C', 'C', 'S', 'Q', 'W', 'G', 'F', 'C', 'G', 'L', 'G', 'S', 'E', 'F', 'C', 'G', 'G', 'G', 'C', 'Q', 'S', 'G', 'A', 'C']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_length(self): """Test getting the number of alignments without parsing the file.""" stream = open(self.path) alignments = Align.parse(stream, "hhr") stream.close() self.assertEqual(len(alignments), 32) class Align_hhr_allx(unittest.TestCase): path = os.path.join("HHsuite", "allx.hhr") def test_reading(self): alignments = Align.parse(self.path, "hhr") self.assertEqual(alignments.metadata["No_of_seqs"], (1, 1)) self.assertAlmostEqual(alignments.metadata["Neff"], 1.0) self.assertEqual(alignments.metadata["Searched_HMMs"], 38388) self.assertEqual(alignments.metadata["Rundate"], "Fri Feb 15 16:24:19 2019") self.assertEqual( alignments.metadata["Command line"], "hhsearch -i allx.fasta -d /pdb70_hhm_db", ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 0.04) self.assertAlmostEqual(alignment.annotations["E-value"], 3.4e04) self.assertAlmostEqual(alignment.annotations["Score"], -0.01) self.assertAlmostEqual(alignment.annotations["Identities"], 0) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.427) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "Only X amino acids") self.assertEqual(alignment.query.seq[38:39], "X") self.assertEqual(alignment[1], "X") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~ ", ) self.assertEqual(alignment.target.id, "1klr_A") self.assertEqual(alignment.target.seq[23:24], "T") self.assertEqual(alignment.target.annotations["hmm_name"], "1klr_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Zinc finger Y-chromosomal protein; transcription; NMR {Synthetic} SCOP: g.37.1.1 PDB: 5znf_A 1kls_A 1xrz_A* 7znf_A", ) self.assertEqual(alignment[0], "T") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " H ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " H ", ) self.assertEqual( str(alignment), """\ 1klr_A 23 T 24 0 . 1 Only X am 38 X 39 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23, 24], [38, 39]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), np.array([["T"], ["X"]], dtype="U") ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 0.04) self.assertAlmostEqual(alignment.annotations["E-value"], 3.4e04) self.assertAlmostEqual(alignment.annotations["Score"], 0.00) self.assertAlmostEqual(alignment.annotations["Identities"], 0) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.158) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "Only X amino acids") self.assertEqual(alignment.query.seq[3:4], "X") self.assertEqual(alignment[1], "X") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~ ", ) self.assertEqual(alignment.target.id, "5ion_A") self.assertEqual(alignment.target.seq[9:10], "G") self.assertEqual(alignment.target.annotations["hmm_name"], "5ion_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Zinc finger and BTB domain-containing protein 17; C2H2 zinc finger, MIZ-1, ZBTB17, transcription factor, trans; NMR {Homo sapiens}", ) self.assertEqual(alignment[0], "G") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " T ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " C ", ) self.assertEqual( str(alignment), """\ 5ion_A 9 G 10 0 . 1 Only X am 3 X 4 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 9, 10], [ 3, 4]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), np.array([["G"], ["X"]], dtype="U") ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 0.04) self.assertAlmostEqual(alignment.annotations["E-value"], 3.4e04) self.assertAlmostEqual(alignment.annotations["Score"], 0.04) self.assertAlmostEqual(alignment.annotations["Identities"], 0) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.575) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "Only X amino acids") self.assertEqual(alignment.query.seq[3:4], "X") self.assertEqual(alignment[1], "X") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~ ", ) self.assertEqual(alignment.target.id, "2jvx_A") self.assertEqual(alignment.target.seq[0:1], "S") self.assertEqual(alignment.target.annotations["hmm_name"], "2jvx_A") self.assertEqual( alignment.target.annotations["hmm_description"], "NF-kappa-B essential modulator; CCHC classical zinc finger, NEMO zinc finger, beta-BETA- alpha fold, coiled coil, cytoplasm, disease mutation; NMR {Synthetic} PDB: 2jvy_A", ) self.assertEqual(alignment[0], "S") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "C ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "C ", ) self.assertEqual( str(alignment), """\ 2jvx_A 0 S 1 0 . 1 Only X am 3 X 4 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 1], [3, 4]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), np.array([["S"], ["X"]], dtype="U") ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 0.04) self.assertAlmostEqual(alignment.annotations["E-value"], 3.4e04) self.assertAlmostEqual(alignment.annotations["Score"], 0.03) self.assertAlmostEqual(alignment.annotations["Identities"], 0) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.158) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "Only X amino acids") self.assertEqual(alignment.query.seq[3:4], "X") self.assertEqual(alignment[1], "X") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~ ", ) self.assertEqual(alignment.target.id, "2ab3_A") self.assertEqual(alignment.target.seq[10:11], "G") self.assertEqual(alignment.target.annotations["hmm_name"], "2ab3_A") self.assertEqual( alignment.target.annotations["hmm_description"], "ZNF29; zinc finger protein, beta BETA alpha, RREIIB-TR, RNA binding protein; NMR {Escherichia coli} SCOP: k.12.1.1 PDB: 2ab7_A", ) self.assertEqual(alignment[0], "G") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " C ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " C ", ) self.assertEqual( str(alignment), """\ 2ab3_A 10 G 11 0 . 1 Only X am 3 X 4 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10, 11], [ 3, 4]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), np.array([["G"], ["X"]], dtype="U") ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 0.04) self.assertAlmostEqual(alignment.annotations["E-value"], 3.5e04) self.assertAlmostEqual(alignment.annotations["Score"], 0.02) self.assertAlmostEqual(alignment.annotations["Identities"], 0) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.427) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "Only X amino acids") self.assertEqual(alignment.query.seq[3:4], "X") self.assertEqual(alignment[1], "X") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~ ", ) self.assertEqual(alignment.target.id, "1sp2_A") self.assertEqual(alignment.target.seq[5:6], "T") self.assertEqual(alignment.target.annotations["hmm_name"], "1sp2_A") self.assertEqual( alignment.target.annotations["hmm_description"], "SP1F2; zinc finger, transcription activation; NMR {Homo sapiens} SCOP: g.37.1.1 PDB: 1va2_A", ) self.assertEqual(alignment[0], "T") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " C ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " C ", ) self.assertEqual( str(alignment), """\ 1sp2_A 5 T 6 0 . 1 Only X am 3 X 4 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[5, 6], [3, 4]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), np.array([["T"], ["X"]], dtype="U") ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 0.04) self.assertAlmostEqual(alignment.annotations["E-value"], 3.5e04) self.assertAlmostEqual(alignment.annotations["Score"], 0.00) self.assertAlmostEqual(alignment.annotations["Identities"], 0) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.251) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "Only X amino acids") self.assertEqual(alignment.query.seq[37:38], "X") self.assertEqual(alignment[1], "X") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~ ", ) self.assertEqual(alignment.target.id, "2lvr_A") self.assertEqual(alignment.target.seq[28:29], "E") self.assertEqual(alignment.target.annotations["hmm_name"], "2lvr_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Zinc finger and BTB domain-containing protein 17; C2H2 zinc finger, classical zinc finger, transcription; NMR {Homo sapiens}", ) self.assertEqual(alignment[0], "E") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " C ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " C ", ) self.assertEqual( str(alignment), """\ 2lvr_A 28 E 29 0 . 1 Only X am 37 X 38 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[28, 29], [37, 38]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), np.array([["E"], ["X"]], dtype="U") ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 0.04) self.assertAlmostEqual(alignment.annotations["E-value"], 3.5e04) self.assertAlmostEqual(alignment.annotations["Score"], 0.02) self.assertAlmostEqual(alignment.annotations["Identities"], 0) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.155) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "Only X amino acids") self.assertEqual(alignment.query.seq[1:2], "X") self.assertEqual(alignment[1], "X") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~ ", ) self.assertEqual(alignment.target.id, "2kvf_A") self.assertEqual(alignment.target.seq[0:1], "M") self.assertEqual(alignment.target.annotations["hmm_name"], "2kvf_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}", ) self.assertEqual(alignment[0], "M") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "C ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "C ", ) self.assertEqual( str(alignment), """\ 2kvf_A 0 M 1 0 . 1 Only X am 1 X 2 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 1], [1, 2]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), np.array([["M"], ["X"]], dtype="U") ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 0.03) self.assertAlmostEqual(alignment.annotations["E-value"], 3.6e04) self.assertAlmostEqual(alignment.annotations["Score"], 0.02) self.assertAlmostEqual(alignment.annotations["Identities"], 0) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.170) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "Only X amino acids") self.assertEqual(alignment.query.seq[35:36], "X") self.assertEqual(alignment[1], "X") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~ ", ) self.assertEqual(alignment.target.id, "1dsq_A") self.assertEqual(alignment.target.seq[16:17], "D") self.assertEqual(alignment.target.annotations["hmm_name"], "1dsq_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1", ) self.assertEqual(alignment[0], "D") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " T " ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " h " ) self.assertEqual( str(alignment), """\ 1dsq_A 16 D 17 0 . 1 Only X am 35 X 36 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[16, 17], [35, 36]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), np.array([["D"], ["X"]], dtype="U") ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 0.03) self.assertAlmostEqual(alignment.annotations["E-value"], 3.6e04) self.assertAlmostEqual(alignment.annotations["Score"], 0.03) self.assertAlmostEqual(alignment.annotations["Identities"], 0) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.209) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "Only X amino acids") self.assertEqual(alignment.query.seq[35:36], "X") self.assertEqual(alignment[1], "X") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~", ) self.assertEqual(alignment.target.id, "5a7u_A") self.assertEqual(alignment.target.seq[28:29], "N") self.assertEqual(alignment.target.annotations["hmm_name"], "5a7u_A") self.assertEqual( alignment.target.annotations["hmm_description"], "ADR1, regulatory protein ADR1; protein folding, translation, ribosome, zinc finger, SECM, translational arrest peptide, cryo-EM; 4.80A {Saccharomyces cerevisiae} PDB: 1paa_A", ) self.assertEqual(alignment[0], "N") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " C", ) self.assertEqual( str(alignment), """\ 5a7u_A 28 N 29 0 . 1 Only X am 35 X 36 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[28, 29], [35, 36]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), np.array([["N"], ["X"]], dtype="U") ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 0.03) self.assertAlmostEqual(alignment.annotations["E-value"], 3.6e04) self.assertAlmostEqual(alignment.annotations["Score"], 0.03) self.assertAlmostEqual(alignment.annotations["Identities"], 0) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.170) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertEqual(alignment.query.id, "Only X amino acids") self.assertEqual(alignment.query.seq[3:4], "X") self.assertEqual(alignment[1], "X") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~ ", ) self.assertEqual(alignment.target.id, "1zfd_A") self.assertEqual(alignment.target.seq[0:1], "D") self.assertEqual(alignment.target.annotations["hmm_name"], "1zfd_A") self.assertEqual( alignment.target.annotations["hmm_description"], "SWI5; DNA binding motif, zinc finger DNA binding domain; NMR {Saccharomyces cerevisiae} SCOP: g.37.1.1", ) self.assertEqual(alignment[0], "D") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "C ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "C ", ) self.assertEqual( str(alignment), """\ 1zfd_A 0 D 1 0 . 1 Only X am 3 X 4 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 1], [3, 4]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), np.array([["D"], ["X"]], dtype="U") ) ) with self.assertRaises(StopIteration): next(alignments) def test_length(self): """Test getting the number of alignments without parsing the file.""" stream = open(self.path) alignments = Align.parse(stream, "hhr") stream.close() self.assertEqual(len(alignments), 10) class Align_hhr_4p79_hhsearch_server_NOssm(unittest.TestCase): path = os.path.join("HHsuite", "4p79_hhsearch_server_NOssm.hhr") def test_reading(self): alignments = Align.parse(self.path, "hhr") self.assertEqual(alignments.metadata["No_of_seqs"], (110, 1051)) self.assertAlmostEqual(alignments.metadata["Neff"], 10.453) self.assertEqual(alignments.metadata["Searched_HMMs"], 46616) self.assertEqual(alignments.metadata["Rundate"], "Thu Nov 29 16:33:45 2018") self.assertEqual( alignments.metadata["Command line"], "hhsearch -cpu 8 -i ../results/full.a3m -d /cluster/toolkit/production/databases/hh-suite/mmcif70/pdb70 -o ../results/4P79_1.hhr -oa3m ../results/4P79_1.a3m -p 50 -Z 250 -loc -z 1 -b 1 -B 250 -ssm 0 -sc 1 -seq 1 -dbstrlen 10000 -norealign -maxres 32000 -contxt /cluster/toolkit/production/bioprogs/tools/hh-suite-build/data/context_data.crf", ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.94) self.assertAlmostEqual(alignment.annotations["E-value"], 6.8e-32, places=33) self.assertAlmostEqual(alignment.annotations["Score"], 194.63) self.assertAlmostEqual(alignment.annotations["Identities"], 100) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.536) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 10.300) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CcHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCcccccCCCccccceEEeccchhhhccCCCCeecccchhHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCceecchHHHHHHHHHHHHHHHHHHHhhhhhcCCCCcccC", ) self.assertEqual(alignment.query.id, "4P79:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:198], "GSEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR", ) self.assertEqual( alignment[1], "GSEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~m~~~~l~~~~~~l~~~a~~l~~~a~~t~~W~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~sf~l~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~~~m~~~~~~~~~~~l~~~a~~l~~va~~tp~W~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~g~s~~l~~~a~~l~~~~~i~~~~~~~~~~~~~~~~~", ) self.assertEqual(alignment.target.id, "4P79_A") self.assertEqual( alignment.target.seq[0:198], "GSEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR", ) self.assertEqual(alignment.target.annotations["hmm_name"], "4P79_A") self.assertEqual( alignment.target.annotations["hmm_description"], "cell adhesion protein; cell adhesion, tight junction, membrane; HET: OLC, MSE; 2.4A {Mus musculus}", ) self.assertEqual( alignment[0], "GSEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CHHHHHHHHHHHHHHHHHHHHHHHHHHTCSCSEEECCEEEECSSEEEEECTTSCEEEEECCHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCSCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHTC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CChHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccccccCCCccccceEEeccchhhhhcCCCCcccccchHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcCCCCCCcccchhHHHHHHHHHHHHHHHHHHHhchhccCCCCccCC", ) self.assertEqual( str(alignment), """\ 4P79_A 0 GSEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDS 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 4P79:A|PD 0 GSEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDS 4P79_A 60 LGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKL 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 4P79:A|PD 60 LGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKL 4P79_A 120 LAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGG 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 4P79:A|PD 120 LAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGG 4P79_A 180 ICVFSTAAASSKEEPATR 198 180 |||||||||||||||||| 198 4P79:A|PD 180 ICVFSTAAASSKEEPATR 198 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 198], [ 0, 198]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'S', 'E', 'F', 'M', 'S', 'V', 'A', 'V', 'E', 'T', 'F', 'G', 'F', 'F', 'M', 'S', 'A', 'L', 'G', 'L', 'L', 'M', 'L', 'G', 'L', 'T', 'L', 'S', 'N', 'S', 'Y', 'W', 'R', 'V', 'S', 'T', 'V', 'H', 'G', 'N', 'V', 'I', 'T', 'T', 'N', 'T', 'I', 'F', 'E', 'N', 'L', 'W', 'Y', 'S', 'C', 'A', 'T', 'D', 'S', 'L', 'G', 'V', 'S', 'N', 'C', 'W', 'D', 'F', 'P', 'S', 'M', 'L', 'A', 'L', 'S', 'G', 'Y', 'V', 'Q', 'G', 'C', 'R', 'A', 'L', 'M', 'I', 'T', 'A', 'I', 'L', 'L', 'G', 'F', 'L', 'G', 'L', 'F', 'L', 'G', 'M', 'V', 'G', 'L', 'R', 'A', 'T', 'N', 'V', 'G', 'N', 'M', 'D', 'L', 'S', 'K', 'K', 'A', 'K', 'L', 'L', 'A', 'I', 'A', 'G', 'T', 'L', 'H', 'I', 'L', 'A', 'G', 'A', 'C', 'G', 'M', 'V', 'A', 'I', 'S', 'W', 'Y', 'A', 'V', 'N', 'I', 'T', 'T', 'D', 'F', 'F', 'N', 'P', 'L', 'Y', 'A', 'G', 'T', 'K', 'Y', 'E', 'L', 'G', 'P', 'A', 'L', 'Y', 'L', 'G', 'W', 'S', 'A', 'S', 'L', 'L', 'S', 'I', 'L', 'G', 'G', 'I', 'C', 'V', 'F', 'S', 'T', 'A', 'A', 'A', 'S', 'S', 'K', 'E', 'E', 'P', 'A', 'T', 'R'], ['G', 'S', 'E', 'F', 'M', 'S', 'V', 'A', 'V', 'E', 'T', 'F', 'G', 'F', 'F', 'M', 'S', 'A', 'L', 'G', 'L', 'L', 'M', 'L', 'G', 'L', 'T', 'L', 'S', 'N', 'S', 'Y', 'W', 'R', 'V', 'S', 'T', 'V', 'H', 'G', 'N', 'V', 'I', 'T', 'T', 'N', 'T', 'I', 'F', 'E', 'N', 'L', 'W', 'Y', 'S', 'C', 'A', 'T', 'D', 'S', 'L', 'G', 'V', 'S', 'N', 'C', 'W', 'D', 'F', 'P', 'S', 'M', 'L', 'A', 'L', 'S', 'G', 'Y', 'V', 'Q', 'G', 'C', 'R', 'A', 'L', 'M', 'I', 'T', 'A', 'I', 'L', 'L', 'G', 'F', 'L', 'G', 'L', 'F', 'L', 'G', 'M', 'V', 'G', 'L', 'R', 'A', 'T', 'N', 'V', 'G', 'N', 'M', 'D', 'L', 'S', 'K', 'K', 'A', 'K', 'L', 'L', 'A', 'I', 'A', 'G', 'T', 'L', 'H', 'I', 'L', 'A', 'G', 'A', 'C', 'G', 'M', 'V', 'A', 'I', 'S', 'W', 'Y', 'A', 'V', 'N', 'I', 'T', 'T', 'D', 'F', 'F', 'N', 'P', 'L', 'Y', 'A', 'G', 'T', 'K', 'Y', 'E', 'L', 'G', 'P', 'A', 'L', 'Y', 'L', 'G', 'W', 'S', 'A', 'S', 'L', 'L', 'S', 'I', 'L', 'G', 'G', 'I', 'C', 'V', 'F', 'S', 'T', 'A', 'A', 'A', 'S', 'S', 'K', 'E', 'E', 'P', 'A', 'T', 'R']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.88) self.assertAlmostEqual(alignment.annotations["E-value"], 1.8e-27, places=28) self.assertAlmostEqual(alignment.annotations["Score"], 169.81) self.assertAlmostEqual(alignment.annotations["Identities"], 38) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.775) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 10.300) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHHHHHHhCcCCcccccCCCccccceEEeccchhhhccCCCCeecccchhHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCceecchHHHHHHHHHHHHHHHHHHHhh ", ) self.assertEqual(alignment.query.id, "4P79:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[3:186], "FMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFST", ) self.assertEqual( alignment[1], "FMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGN-VITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLY-AGTKYELGPALYLGWSASLLSILGGICVFST", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " m~~~~l~~~~~~l~~~a~~l~~~a~~t~~W~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~sf~l~~~~~~l~~~~~~l~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "M~~~~~~~~~~~l~~~~~~l~i~a~~tp~W~~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~s~~l~~~~~~l~~~~~~l~~~~", ) self.assertEqual(alignment.target.id, "3X29_C") self.assertEqual( alignment.target.seq[0:185], "MANSGLQLLGYFLALGGWVGIIASTALPQWKQSSYAGDAIITAVGLYEGLWMSCASQSTGQVQCKLYDSLLALDGHIQSARALMVVAVLLGFVAMVLSVVGMKATRVGDSNPTAKSRVAISGGALFLLAGLCTLTAVSWYATLVTQEFFNPSTPVNARYEFGPALFVGWASAGLAMLGGSFLAAT", ) self.assertEqual(alignment.target.annotations["hmm_name"], "3X29_C") self.assertEqual( alignment.target.annotations["hmm_description"], "Claudin-19, Heat-labile enterotoxin B chain; TOXIN-CELL ADHESION COMPLEX, TIGHT JUNCTION; 3.7A {Mus musculus}; Related PDB entries: 3X29_A", ) self.assertEqual( alignment[0], "MANSGLQLLGYFLALGGWVGIIASTALPQWKQSSYAGDAIITAVGLYEGLWMSCASQSTGQVQCKLYDSLLALDGHIQSARALMVVAVLLGFVAMVLSVVGMKATRVGDSNPTAKSRVAISGGALFLLAGLCTLTAVSWYATLVTQEFFNPSTPVNARYEFGPALFVGWASAGLAMLGGSFLAAT", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CHHHHHHHHHHHHHHHHHHHHHHCSCSEEEEECSSSSSSCEEEEECSSEEECCCCCEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTSCTTEEEEECTHHHHHHHHHHHHHHHHHHHHTC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "ChhHHHHHHHHHHHHHHHHHHHHHHhCchhhhcccCCCcccccceeeeeccchhhhcCCCcEEceechhHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHcchhhhcCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccHHHHHHHHHHHHHHHHHHHHhcC", ) self.assertEqual( str(alignment), """\ 3X29_C 0 MANSGLQLLGYFLALGGWVGIIASTALPQWKQSSYAGDAIITAVGLYEGLWMSCASQSTG 0 .........|.|....|............|..|...|.-.||.....|.||.|||..|.| 4P79:A|PD 3 FMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGN-VITTNTIFENLWYSCATDSLG 3X29_C 60 QVQCKLYDSLLALDGHIQSARALMVVAVLLGFVAMVLSVVGMKATRVGDSNPTAKSRVAI 60 ...|....|.|||.|..|..||||..|.||||....|..||..||.||......|..... 4P79:A|PD 62 VSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLA 3X29_C 120 SGGALFLLAGLCTLTAVSWYATLVTQEFFNPSTPVNARYEFGPALFVGWASAGLAMLGGS 120 ..|.|..|||.|...|.||||...|..||||..-....||.||||..||....|..|||. 4P79:A|PD 122 IAGTLHILAGACGMVAISWYAVNITTDFFNPLY-AGTKYELGPALYLGWSASLLSILGGI 3X29_C 180 FLAAT 185 180 ....| 185 4P79:A|PD 181 CVFST 186 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 38, 39, 153, 154, 185], [ 3, 41, 41, 155, 155, 186]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['M', 'A', 'N', 'S', 'G', 'L', 'Q', 'L', 'L', 'G', 'Y', 'F', 'L', 'A', 'L', 'G', 'G', 'W', 'V', 'G', 'I', 'I', 'A', 'S', 'T', 'A', 'L', 'P', 'Q', 'W', 'K', 'Q', 'S', 'S', 'Y', 'A', 'G', 'D', 'A', 'I', 'I', 'T', 'A', 'V', 'G', 'L', 'Y', 'E', 'G', 'L', 'W', 'M', 'S', 'C', 'A', 'S', 'Q', 'S', 'T', 'G', 'Q', 'V', 'Q', 'C', 'K', 'L', 'Y', 'D', 'S', 'L', 'L', 'A', 'L', 'D', 'G', 'H', 'I', 'Q', 'S', 'A', 'R', 'A', 'L', 'M', 'V', 'V', 'A', 'V', 'L', 'L', 'G', 'F', 'V', 'A', 'M', 'V', 'L', 'S', 'V', 'V', 'G', 'M', 'K', 'A', 'T', 'R', 'V', 'G', 'D', 'S', 'N', 'P', 'T', 'A', 'K', 'S', 'R', 'V', 'A', 'I', 'S', 'G', 'G', 'A', 'L', 'F', 'L', 'L', 'A', 'G', 'L', 'C', 'T', 'L', 'T', 'A', 'V', 'S', 'W', 'Y', 'A', 'T', 'L', 'V', 'T', 'Q', 'E', 'F', 'F', 'N', 'P', 'S', 'T', 'P', 'V', 'N', 'A', 'R', 'Y', 'E', 'F', 'G', 'P', 'A', 'L', 'F', 'V', 'G', 'W', 'A', 'S', 'A', 'G', 'L', 'A', 'M', 'L', 'G', 'G', 'S', 'F', 'L', 'A', 'A', 'T'], ['F', 'M', 'S', 'V', 'A', 'V', 'E', 'T', 'F', 'G', 'F', 'F', 'M', 'S', 'A', 'L', 'G', 'L', 'L', 'M', 'L', 'G', 'L', 'T', 'L', 'S', 'N', 'S', 'Y', 'W', 'R', 'V', 'S', 'T', 'V', 'H', 'G', 'N', '-', 'V', 'I', 'T', 'T', 'N', 'T', 'I', 'F', 'E', 'N', 'L', 'W', 'Y', 'S', 'C', 'A', 'T', 'D', 'S', 'L', 'G', 'V', 'S', 'N', 'C', 'W', 'D', 'F', 'P', 'S', 'M', 'L', 'A', 'L', 'S', 'G', 'Y', 'V', 'Q', 'G', 'C', 'R', 'A', 'L', 'M', 'I', 'T', 'A', 'I', 'L', 'L', 'G', 'F', 'L', 'G', 'L', 'F', 'L', 'G', 'M', 'V', 'G', 'L', 'R', 'A', 'T', 'N', 'V', 'G', 'N', 'M', 'D', 'L', 'S', 'K', 'K', 'A', 'K', 'L', 'L', 'A', 'I', 'A', 'G', 'T', 'L', 'H', 'I', 'L', 'A', 'G', 'A', 'C', 'G', 'M', 'V', 'A', 'I', 'S', 'W', 'Y', 'A', 'V', 'N', 'I', 'T', 'T', 'D', 'F', 'F', 'N', 'P', 'L', 'Y', '-', 'A', 'G', 'T', 'K', 'Y', 'E', 'L', 'G', 'P', 'A', 'L', 'Y', 'L', 'G', 'W', 'S', 'A', 'S', 'L', 'L', 'S', 'I', 'L', 'G', 'G', 'I', 'C', 'V', 'F', 'S', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.84) self.assertAlmostEqual(alignment.annotations["E-value"], 1.2e-25, places=26) self.assertAlmostEqual(alignment.annotations["Score"], 176.50) self.assertAlmostEqual(alignment.annotations["Identities"], 37) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.639) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.700) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " cHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCcccccCCCccccceEEeccchhhhccCCCCeecccchhHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCceecchHHHHHHHHHHHHHHHHHHHhhhhhcCCCCccc ", ) self.assertEqual(alignment.query.id, "4P79:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:197], "SEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPAT", ) self.assertEqual( alignment[1], "SEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGN-VITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLY-AGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPAT", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~m~~~~l~~~~~~l~~~a~~l~~~a~~t~~W~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~sf~l~~~~~~l~~~~~~l~~~~~~~~~~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~m~~~~~~~~~~~l~~~a~il~~va~~tp~W~~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~i~s~i~~~~a~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~GwS~~l~~~s~~l~lia~~l~~~~~~~~~~~~~~~", ) self.assertEqual(alignment.target.id, "5B2G_A") self.assertEqual( alignment.target.seq[167:364], "KGMASMGLQVMGIALAVLGWLAVMLCCALPMWRVTAFIGSNIVTSQTIWEGLWMNCVVQSTGQMQCKVYDSLLALPQDLQAARALVIISIIVAALGVLLSVVGGKCTNCLEDESAKAKTMIVAGVVFLLAGLMVIVPVSWTAHNIIQDFYNPLVASGQKREMGASLYVGWAASGLLLLGGGLLCCSGPSSGENLYFQ", ) self.assertEqual(alignment.target.annotations["hmm_name"], "5B2G_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Endolysin,Claudin-4 (E.C.3.2.1.17), Heat-labile enterotoxin B; Membrane protein, Complex, Cell-free protein; HET: MSE; 3.5A {Enterobacteria phage T4}; Related PDB entries: 5B2G_E 5B2G_C 5B2G_G", ) self.assertEqual( alignment[0], "KGMASMGLQVMGIALAVLGWLAVMLCCALPMWRVTAFIGSNIVTSQTIWEGLWMNCVVQSTGQMQCKVYDSLLALPQDLQAARALVIISIIVAALGVLLSVVGGKCTNCLED-ESAKAKTMIVAGVVFLLAGLMVIVPVSWTAHNIIQDFYNPLVASGQKREMGASLYVGWAASGLLLLGGGLLCCSGPSSGENLYFQ", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCHHHHHHHHHHHHHHHHHHHHSSCSEEEEECSTTCSSCEEEEECSSEEEEEESSSSCEEEECCSSCSCCHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTSCSSEEEEECTHHHHHHHHHHHHHHHHHHHHCC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " hhhHHHHHHHHHHHHHHHHHHHHHHHHhCchhhhhcccCCcccCceeEEEeccchheeecCCceEeeechhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCChhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCcccCCCCCcccchHHHHHHHHHHHHHHHHHHHHhcCCCCCCccccC", ) self.assertEqual( str(alignment), """\ 5B2G_A 167 KGMASMGLQVMGIALAVLGWLAVMLCCALPMWRVTAFIGSNIVTSQTIWEGLWMNCVVQS 0 ....|......|.....||.|...|......|||....|.-..|..||.|.||..|...| 4P79:A|PD 1 SEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGN-VITTNTIFENLWYSCATDS 5B2G_A 227 TGQMQCKVYDSLLALPQDLQAARALVIISIIVAALGVLLSVVGGKCTNCLED-ESAKAKT 60 .|...|....|.|||....|..|||.|..|....||..|..||...||....-.|.|||. 4P79:A|PD 60 LGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKL 5B2G_A 286 MIVAGVVFLLAGLMVIVPVSWTAHNIIQDFYNPLVASGQKREMGASLYVGWAASGLLLLG 120 ...||....|||....|..||.|.||..||.|||.-.|.|.|.|..||.||.||.|..|| 4P79:A|PD 120 LAIAGTLHILAGACGMVAISWYAVNITTDFFNPLY-AGTKYELGPALYLGWSASLLSILG 5B2G_A 346 GGLLCCSGPSSGENLYFQ 364 180 |.........|....... 198 4P79:A|PD 179 GICVFSTAAASSKEEPAT 197 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[167, 207, 208, 279, 279, 321, 322, 364], [ 1, 41, 41, 112, 113, 155, 155, 197]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'G', 'M', 'A', 'S', 'M', 'G', 'L', 'Q', 'V', 'M', 'G', 'I', 'A', 'L', 'A', 'V', 'L', 'G', 'W', 'L', 'A', 'V', 'M', 'L', 'C', 'C', 'A', 'L', 'P', 'M', 'W', 'R', 'V', 'T', 'A', 'F', 'I', 'G', 'S', 'N', 'I', 'V', 'T', 'S', 'Q', 'T', 'I', 'W', 'E', 'G', 'L', 'W', 'M', 'N', 'C', 'V', 'V', 'Q', 'S', 'T', 'G', 'Q', 'M', 'Q', 'C', 'K', 'V', 'Y', 'D', 'S', 'L', 'L', 'A', 'L', 'P', 'Q', 'D', 'L', 'Q', 'A', 'A', 'R', 'A', 'L', 'V', 'I', 'I', 'S', 'I', 'I', 'V', 'A', 'A', 'L', 'G', 'V', 'L', 'L', 'S', 'V', 'V', 'G', 'G', 'K', 'C', 'T', 'N', 'C', 'L', 'E', 'D', '-', 'E', 'S', 'A', 'K', 'A', 'K', 'T', 'M', 'I', 'V', 'A', 'G', 'V', 'V', 'F', 'L', 'L', 'A', 'G', 'L', 'M', 'V', 'I', 'V', 'P', 'V', 'S', 'W', 'T', 'A', 'H', 'N', 'I', 'I', 'Q', 'D', 'F', 'Y', 'N', 'P', 'L', 'V', 'A', 'S', 'G', 'Q', 'K', 'R', 'E', 'M', 'G', 'A', 'S', 'L', 'Y', 'V', 'G', 'W', 'A', 'A', 'S', 'G', 'L', 'L', 'L', 'L', 'G', 'G', 'G', 'L', 'L', 'C', 'C', 'S', 'G', 'P', 'S', 'S', 'G', 'E', 'N', 'L', 'Y', 'F', 'Q'], ['S', 'E', 'F', 'M', 'S', 'V', 'A', 'V', 'E', 'T', 'F', 'G', 'F', 'F', 'M', 'S', 'A', 'L', 'G', 'L', 'L', 'M', 'L', 'G', 'L', 'T', 'L', 'S', 'N', 'S', 'Y', 'W', 'R', 'V', 'S', 'T', 'V', 'H', 'G', 'N', '-', 'V', 'I', 'T', 'T', 'N', 'T', 'I', 'F', 'E', 'N', 'L', 'W', 'Y', 'S', 'C', 'A', 'T', 'D', 'S', 'L', 'G', 'V', 'S', 'N', 'C', 'W', 'D', 'F', 'P', 'S', 'M', 'L', 'A', 'L', 'S', 'G', 'Y', 'V', 'Q', 'G', 'C', 'R', 'A', 'L', 'M', 'I', 'T', 'A', 'I', 'L', 'L', 'G', 'F', 'L', 'G', 'L', 'F', 'L', 'G', 'M', 'V', 'G', 'L', 'R', 'A', 'T', 'N', 'V', 'G', 'N', 'M', 'D', 'L', 'S', 'K', 'K', 'A', 'K', 'L', 'L', 'A', 'I', 'A', 'G', 'T', 'L', 'H', 'I', 'L', 'A', 'G', 'A', 'C', 'G', 'M', 'V', 'A', 'I', 'S', 'W', 'Y', 'A', 'V', 'N', 'I', 'T', 'T', 'D', 'F', 'F', 'N', 'P', 'L', 'Y', '-', 'A', 'G', 'T', 'K', 'Y', 'E', 'L', 'G', 'P', 'A', 'L', 'Y', 'L', 'G', 'W', 'S', 'A', 'S', 'L', 'L', 'S', 'I', 'L', 'G', 'G', 'I', 'C', 'V', 'F', 'S', 'T', 'A', 'A', 'A', 'S', 'S', 'K', 'E', 'E', 'P', 'A', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.82) self.assertAlmostEqual(alignment.annotations["E-value"], 1.1e-24, places=25) self.assertAlmostEqual(alignment.annotations["Score"], 168.32) self.assertAlmostEqual(alignment.annotations["Identities"], 15) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.164) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CcHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCcccccCCCccccceEEeccchhhhccCCCCeecccchhHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCceecchHHHHHHHHHHHHHHHHHHHhhhhhcCCCCcccC", ) self.assertEqual(alignment.query.id, "4P79:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:198], "GSEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR", ) self.assertEqual( alignment[1], "GSEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGN-----------VITTNTIFENLWYSCATDSLGVSNCWDFPSMLAL-----------SGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~m~~~~l~~~~~~l~~~a~~l~~~a~~t~~W~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~sf~l~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "m~~~~r~~l~~l~~vl~~~a~vL~~ia~~tp~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~C~~~~~f~~~~~~~~~~~~~~~~~~r~~~~f~ilsl~l~~l~~l~~~~~~~~~~~~~~~~~agil~~lAgl~~~i~vily~~~~~~~~~~~~~~~~~~~~GwSf~~~~~s~~l~~la~vl~v~~~~~~~~~~~~~~ ", ) self.assertEqual(alignment.target.id, "5KK2_G") self.assertEqual( alignment.target.seq[0:212], "MGLFDRGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSENETSKKNEEVMTHSGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLCIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLRATA", ) self.assertEqual(alignment.target.annotations["hmm_name"], "5KK2_G") self.assertEqual( alignment.target.annotations["hmm_description"], "Glutamate receptor 2, Voltage-dependent calcium; Tetrameric, ionotropic, glutamate receptors, GluA2; 7.3A {Rattus norvegicus}; Related PDB entries: 5VOT_E 5VOT_H 5VOU_H 5KK2_H 5VOV_E 5VOT_F 5KK2_F 5VOT_G 5VOV_G 5VOU_E 5VOV_H 5VOU_G 5VOV_F 5VOU_F 5KK2_E", ) self.assertEqual( alignment[0], "MGLFDRGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSENETSKKNEEVMTHSGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLCIAASEFY--------KTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLRATA", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CHHHHHHHHHHHHHHHHHHHHHHCCCCCBCCCCCCEECCSSEEEECCCCEEEECCCCCCCCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CchhhHHHHHHHHHHHHHHHHHHHHHHHhcCCceeeecccCCCCCcccccccccceeeeeccccchhccccccCCceeeccCCCCCccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCccCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHH ", ) self.assertEqual( str(alignment), """\ 5KK2_G 0 MGLFDRGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSENETSKKNEEVMTH 0 ...|...........................||..|.....-----------........ 4P79:A|PD 0 GSEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGN-----------VITTNTIF 5KK2_G 60 SGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGL 60 ..||..|.........|.........-----------...|.......|....|.|.|.. 4P79:A|PD 49 ENLWYSCATDSLGVSNCWDFPSMLAL-----------SGYVQGCRALMITAILLGFLGLF 5KK2_G 120 CIAASEFY--------KTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKN 120 ........--------.........||.....||......|..|......|......... 4P79:A|PD 98 LGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGT 5KK2_G 172 SYSYGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLRATA 212 180 .|..|...|.|..........|...........|...||. 220 4P79:A|PD 158 KYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR 198 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 41, 52, 86, 97, 128, 128, 212], [ 0, 41, 41, 75, 75, 106, 114, 198]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['M', 'G', 'L', 'F', 'D', 'R', 'G', 'V', 'Q', 'M', 'L', 'L', 'T', 'T', 'V', 'G', 'A', 'F', 'A', 'A', 'F', 'S', 'L', 'M', 'T', 'I', 'A', 'V', 'G', 'T', 'D', 'Y', 'W', 'L', 'Y', 'S', 'R', 'G', 'V', 'C', 'K', 'T', 'K', 'S', 'V', 'S', 'E', 'N', 'E', 'T', 'S', 'K', 'K', 'N', 'E', 'E', 'V', 'M', 'T', 'H', 'S', 'G', 'L', 'W', 'R', 'T', 'C', 'C', 'L', 'E', 'G', 'N', 'F', 'K', 'G', 'L', 'C', 'K', 'Q', 'I', 'D', 'H', 'F', 'P', 'E', 'D', 'A', 'D', 'Y', 'E', 'A', 'D', 'T', 'A', 'E', 'Y', 'F', 'L', 'R', 'A', 'V', 'R', 'A', 'S', 'S', 'I', 'F', 'P', 'I', 'L', 'S', 'V', 'I', 'L', 'L', 'F', 'M', 'G', 'G', 'L', 'C', 'I', 'A', 'A', 'S', 'E', 'F', 'Y', '-', '-', '-', '-', '-', '-', '-', '-', 'K', 'T', 'R', 'H', 'N', 'I', 'I', 'L', 'S', 'A', 'G', 'I', 'F', 'F', 'V', 'S', 'A', 'G', 'L', 'S', 'N', 'I', 'I', 'G', 'I', 'I', 'V', 'Y', 'I', 'S', 'A', 'N', 'A', 'G', 'D', 'P', 'S', 'K', 'S', 'D', 'S', 'K', 'K', 'N', 'S', 'Y', 'S', 'Y', 'G', 'W', 'S', 'F', 'Y', 'F', 'G', 'A', 'L', 'S', 'F', 'I', 'I', 'A', 'E', 'M', 'V', 'G', 'V', 'L', 'A', 'V', 'H', 'M', 'F', 'I', 'D', 'R', 'H', 'K', 'Q', 'L', 'R', 'A', 'T', 'A'], ['G', 'S', 'E', 'F', 'M', 'S', 'V', 'A', 'V', 'E', 'T', 'F', 'G', 'F', 'F', 'M', 'S', 'A', 'L', 'G', 'L', 'L', 'M', 'L', 'G', 'L', 'T', 'L', 'S', 'N', 'S', 'Y', 'W', 'R', 'V', 'S', 'T', 'V', 'H', 'G', 'N', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'V', 'I', 'T', 'T', 'N', 'T', 'I', 'F', 'E', 'N', 'L', 'W', 'Y', 'S', 'C', 'A', 'T', 'D', 'S', 'L', 'G', 'V', 'S', 'N', 'C', 'W', 'D', 'F', 'P', 'S', 'M', 'L', 'A', 'L', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'S', 'G', 'Y', 'V', 'Q', 'G', 'C', 'R', 'A', 'L', 'M', 'I', 'T', 'A', 'I', 'L', 'L', 'G', 'F', 'L', 'G', 'L', 'F', 'L', 'G', 'M', 'V', 'G', 'L', 'R', 'A', 'T', 'N', 'V', 'G', 'N', 'M', 'D', 'L', 'S', 'K', 'K', 'A', 'K', 'L', 'L', 'A', 'I', 'A', 'G', 'T', 'L', 'H', 'I', 'L', 'A', 'G', 'A', 'C', 'G', 'M', 'V', 'A', 'I', 'S', 'W', 'Y', 'A', 'V', 'N', 'I', 'T', 'T', 'D', 'F', 'F', 'N', 'P', 'L', 'Y', 'A', 'G', 'T', 'K', 'Y', 'E', 'L', 'G', 'P', 'A', 'L', 'Y', 'L', 'G', 'W', 'S', 'A', 'S', 'L', 'L', 'S', 'I', 'L', 'G', 'G', 'I', 'C', 'V', 'F', 'S', 'T', 'A', 'A', 'A', 'S', 'S', 'K', 'E', 'E', 'P', 'A', 'T', 'R']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.81) self.assertAlmostEqual(alignment.annotations["E-value"], 1.2e-24, places=25) self.assertAlmostEqual(alignment.annotations["Score"], 159.28) self.assertAlmostEqual(alignment.annotations["Identities"], 17) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.231) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 10.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " cHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCcccccCCCccccceEEeccchhhhccCCCCeecccchhHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCceecchHHHHHHHHHHHHHHHHHHHhhhhhcCCCCcccC", ) self.assertEqual(alignment.query.id, "4P79:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:198], "SEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR", ) self.assertEqual( alignment[1], "SEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNV--ITTNTIFENLWYSCATDSLG-------------VSNCWDFPSML-----------ALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~m~~~~l~~~~~~l~~~a~~l~~~a~~t~~W~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~sf~l~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "m~~~~~~~~~~~~~l~~~~~~l~~ia~~t~~W~~~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~~~c~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ls~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~s~~l~~~a~~l~~l~~~l~~~~~~~~~~~~~~~~ ", ) self.assertEqual(alignment.target.id, "5GJV_E") self.assertEqual( alignment.target.seq[0:214], "MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKRIALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIMGTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSWSFACACAAFVLLFLGGISLLLFSLPRMPQNPWES", ) self.assertEqual(alignment.target.annotations["hmm_name"], "5GJV_E") self.assertEqual( alignment.target.annotations["hmm_description"], "Voltage-dependent L-type calcium channel subunit; complex, channel, membrane protein; HET: PC1, BMA, NAG; 3.6A {Oryctolagus cuniculus}; Related PDB entries: 3JBR_E 5GJW_E", ) self.assertEqual( alignment[0], "MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKRIALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIMGTICALMAFRK---------KRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSWSFACACAAFVLLFLGGISLLLFSLPRMPQNPWES", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], "CHHHHSHHHHHHHHHHHHHHHHHHHHHHCCCSEEEECCCCEEECCSSCEEEECCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHTTTTCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEECHHHHHHHHHHHHHHHHHHHHHHHHSCCCCSSTTSC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCccccHHHHHHHHHHHHHHHHHHHHHhCcchhhcCCCCCCCCcchheeecccHHHhchhhccCCCCCCccccCCCcccceeeeccCCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcceEeecchHHHHHHHHHHHHHHHHHHHHHHcccCCCCCcchh ", ) self.assertEqual( str(alignment), """\ 5GJV_E 0 MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR 0 .............|....|............|.|...|...--.|.......||..|... 4P79:A|PD 1 SEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNV--ITTNTIFENLWYSCATD 5GJV_E 60 IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM 60 ...-------------..||..|....-----------....|.....|........... 4P79:A|PD 59 SLG-------------VSNCWDFPSML-----------ALSGYVQGCRALMITAILLGFL 5GJV_E 120 GTICALMAFRK---------KRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDT 120 |........|.---------|...||..|......||.|..|.................. 4P79:A|PD 95 GLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLY 5GJV_E 171 VWIEYYYSWSFACACAAFVLLFLGGISLLLFSLPRMPQNPWES 214 180 ....|...........|..|..||||.............|... 223 4P79:A|PD 155 AGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR 198 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 41, 43, 63, 76, 87, 98, 131, 131, 214], [ 1, 42, 42, 62, 62, 73, 73, 106, 115, 198]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['M', 'S', 'P', 'T', 'E', 'A', 'P', 'K', 'V', 'R', 'V', 'T', 'L', 'F', 'C', 'I', 'L', 'V', 'G', 'I', 'V', 'L', 'A', 'M', 'T', 'A', 'V', 'V', 'S', 'D', 'H', 'W', 'A', 'V', 'L', 'S', 'P', 'H', 'M', 'E', 'N', 'H', 'N', 'T', 'T', 'C', 'E', 'A', 'A', 'H', 'F', 'G', 'L', 'W', 'R', 'I', 'C', 'T', 'K', 'R', 'I', 'A', 'L', 'G', 'E', 'D', 'R', 'S', 'C', 'G', 'P', 'I', 'T', 'L', 'P', 'G', 'E', 'K', 'N', 'C', 'S', 'Y', 'F', 'R', 'H', 'F', 'N', 'P', 'G', 'E', 'S', 'S', 'E', 'I', 'F', 'E', 'F', 'T', 'T', 'Q', 'K', 'E', 'Y', 'S', 'I', 'S', 'A', 'A', 'A', 'I', 'S', 'V', 'F', 'S', 'L', 'G', 'F', 'L', 'I', 'M', 'G', 'T', 'I', 'C', 'A', 'L', 'M', 'A', 'F', 'R', 'K', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'K', 'R', 'D', 'Y', 'L', 'L', 'R', 'P', 'A', 'S', 'M', 'F', 'Y', 'V', 'F', 'A', 'G', 'L', 'C', 'L', 'F', 'V', 'S', 'L', 'E', 'V', 'M', 'R', 'Q', 'S', 'V', 'K', 'R', 'M', 'I', 'D', 'S', 'E', 'D', 'T', 'V', 'W', 'I', 'E', 'Y', 'Y', 'Y', 'S', 'W', 'S', 'F', 'A', 'C', 'A', 'C', 'A', 'A', 'F', 'V', 'L', 'L', 'F', 'L', 'G', 'G', 'I', 'S', 'L', 'L', 'L', 'F', 'S', 'L', 'P', 'R', 'M', 'P', 'Q', 'N', 'P', 'W', 'E', 'S'], ['S', 'E', 'F', 'M', 'S', 'V', 'A', 'V', 'E', 'T', 'F', 'G', 'F', 'F', 'M', 'S', 'A', 'L', 'G', 'L', 'L', 'M', 'L', 'G', 'L', 'T', 'L', 'S', 'N', 'S', 'Y', 'W', 'R', 'V', 'S', 'T', 'V', 'H', 'G', 'N', 'V', '-', '-', 'I', 'T', 'T', 'N', 'T', 'I', 'F', 'E', 'N', 'L', 'W', 'Y', 'S', 'C', 'A', 'T', 'D', 'S', 'L', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'V', 'S', 'N', 'C', 'W', 'D', 'F', 'P', 'S', 'M', 'L', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'L', 'S', 'G', 'Y', 'V', 'Q', 'G', 'C', 'R', 'A', 'L', 'M', 'I', 'T', 'A', 'I', 'L', 'L', 'G', 'F', 'L', 'G', 'L', 'F', 'L', 'G', 'M', 'V', 'G', 'L', 'R', 'A', 'T', 'N', 'V', 'G', 'N', 'M', 'D', 'L', 'S', 'K', 'K', 'A', 'K', 'L', 'L', 'A', 'I', 'A', 'G', 'T', 'L', 'H', 'I', 'L', 'A', 'G', 'A', 'C', 'G', 'M', 'V', 'A', 'I', 'S', 'W', 'Y', 'A', 'V', 'N', 'I', 'T', 'T', 'D', 'F', 'F', 'N', 'P', 'L', 'Y', 'A', 'G', 'T', 'K', 'Y', 'E', 'L', 'G', 'P', 'A', 'L', 'Y', 'L', 'G', 'W', 'S', 'A', 'S', 'L', 'L', 'S', 'I', 'L', 'G', 'G', 'I', 'C', 'V', 'F', 'S', 'T', 'A', 'A', 'A', 'S', 'S', 'K', 'E', 'E', 'P', 'A', 'T', 'R']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.79) self.assertAlmostEqual(alignment.annotations["E-value"], 5.7e-24, places=25) self.assertAlmostEqual(alignment.annotations["Score"], 156.78) self.assertAlmostEqual(alignment.annotations["Identities"], 14) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.065) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.000) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHHHHHhCcCCcccccCCCccccceEEeccchhhhccCCCCeecccchhHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCceecchHHHHHHHHHHHHHHHHHHHhhhhhcCCCCcccC", ) self.assertEqual(alignment.query.id, "4P79:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[4:198], "MSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR", ) self.assertEqual( alignment[1], "MSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSL-GVSNCWDFPSMLAL--SGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFN-------PLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~l~~~~~~l~~~a~~l~~~a~~t~~W~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~sf~l~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~~~~~l~~~a~~l~~va~~tp~W~~~~~~~~~~~~~GLw~~C~~~~~~~~~~C~~~~~~~~~~~~~~~~a~~~l~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~lagl~~lv~~ivf~~~~~~~~~~~~~~~~~~~~~~~~~~~GwSf~la~~a~~l~~la~il~~~~~~~~~~~~~~~~ ", ) self.assertEqual(alignment.target.id, "6C14_D") self.assertEqual( alignment.target.seq[27:218], "NSRAVGVMWGTLTICFSVLVMALFIQPYWIGDSVSTPQAGYFGLFSYCVGNVLSSELICKGGPLDFSSIPSRAFKTAMFFVALAMFLIIGSIICFSLFFVCNTATVYKICAWMQLAAATGLMIGCLVYPDGWDSSEVRRMCGEQTGKYTLGHCTIRWAFMLAILSIGDALILSFLAFVLGYRQDKLLPDDY", ) self.assertEqual(alignment.target.annotations["hmm_name"], "6C14_D") self.assertEqual( alignment.target.annotations["hmm_description"], "Protocadherin-15, LHFPL tetraspan subfamily member; PCDH15, LHFPL5, protocadherin, tip link;{Mus musculus}; Related PDB entries: 6C14_B", ) self.assertEqual( alignment[0], "NSRAVGVMWGTLTICFSVLVMALFIQPYWIGDSVSTP----QAGYFGLFSYCVGNVLSSELICKGGPLDFSSIPSRAFKTAMFFVALAMFLIIGSIICFSLFFVC---------NTATVYKICAWMQLAAATGLMIGCLVYPDGWDSSEVRRMCGEQTGKYTLGHCTIRWAFMLAILSIGDALILSFLAFVLGYRQDKLLPDDY", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHHHHHHHHSCSCSEECCCCEECCCSSSCBEECTTCCCCCBCCSSCCSSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHTTTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHHHHHHHHHHHHHHHC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HhHHHHHHHHHHHHHHHHHHHHHHHChHhhCCCCCCCCCceeehhhhhccccCCcceeeecCCCCHhhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHcccCCCCHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhh ", ) self.assertEqual( str(alignment), """\ 6C14_D 27 NSRAVGVMWGTLTICFSVLVMALFIQPYWIGDSVSTP----QAGYFGLFSYCVGNVLSSE 0 .|.||......................||....|...----......|...|....|-.. 4P79:A|PD 4 MSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSL-GV 6C14_D 83 LICKGGPLDFSSIPSRAFKTAMFFVALAMFLIIGSIICFSLFFVC---------NTATVY 60 ..|...|.....--|............|..|..............---------..|... 4P79:A|PD 63 SNCWDFPSMLAL--SGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLL 6C14_D 134 KICAWMQLAAATGLMIGCLVYPDGWDSSEVRRMCGEQTGKYTLGHCTIRWAFMLAILSIG 120 .|.......|....|.....|..........-------..|.........|..|...... 4P79:A|PD 121 AIAGTLHILAGACGMVAISWYAVNITTDFFN-------PLYAGTKYELGPALYLGWSASL 6C14_D 194 DALILSFLAFVLGYRQDKLLPDDY 218 180 .........|.......|..|... 204 4P79:A|PD 174 LSILGGICVFSTAAASSKEEPATR 198 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 27, 64, 64, 80, 81, 95, 97, 128, 128, 165, 172, 218], [ 4, 41, 45, 61, 61, 75, 75, 106, 115, 152, 152, 198]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['N', 'S', 'R', 'A', 'V', 'G', 'V', 'M', 'W', 'G', 'T', 'L', 'T', 'I', 'C', 'F', 'S', 'V', 'L', 'V', 'M', 'A', 'L', 'F', 'I', 'Q', 'P', 'Y', 'W', 'I', 'G', 'D', 'S', 'V', 'S', 'T', 'P', '-', '-', '-', '-', 'Q', 'A', 'G', 'Y', 'F', 'G', 'L', 'F', 'S', 'Y', 'C', 'V', 'G', 'N', 'V', 'L', 'S', 'S', 'E', 'L', 'I', 'C', 'K', 'G', 'G', 'P', 'L', 'D', 'F', 'S', 'S', 'I', 'P', 'S', 'R', 'A', 'F', 'K', 'T', 'A', 'M', 'F', 'F', 'V', 'A', 'L', 'A', 'M', 'F', 'L', 'I', 'I', 'G', 'S', 'I', 'I', 'C', 'F', 'S', 'L', 'F', 'F', 'V', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'N', 'T', 'A', 'T', 'V', 'Y', 'K', 'I', 'C', 'A', 'W', 'M', 'Q', 'L', 'A', 'A', 'A', 'T', 'G', 'L', 'M', 'I', 'G', 'C', 'L', 'V', 'Y', 'P', 'D', 'G', 'W', 'D', 'S', 'S', 'E', 'V', 'R', 'R', 'M', 'C', 'G', 'E', 'Q', 'T', 'G', 'K', 'Y', 'T', 'L', 'G', 'H', 'C', 'T', 'I', 'R', 'W', 'A', 'F', 'M', 'L', 'A', 'I', 'L', 'S', 'I', 'G', 'D', 'A', 'L', 'I', 'L', 'S', 'F', 'L', 'A', 'F', 'V', 'L', 'G', 'Y', 'R', 'Q', 'D', 'K', 'L', 'L', 'P', 'D', 'D', 'Y'], ['M', 'S', 'V', 'A', 'V', 'E', 'T', 'F', 'G', 'F', 'F', 'M', 'S', 'A', 'L', 'G', 'L', 'L', 'M', 'L', 'G', 'L', 'T', 'L', 'S', 'N', 'S', 'Y', 'W', 'R', 'V', 'S', 'T', 'V', 'H', 'G', 'N', 'V', 'I', 'T', 'T', 'N', 'T', 'I', 'F', 'E', 'N', 'L', 'W', 'Y', 'S', 'C', 'A', 'T', 'D', 'S', 'L', '-', 'G', 'V', 'S', 'N', 'C', 'W', 'D', 'F', 'P', 'S', 'M', 'L', 'A', 'L', '-', '-', 'S', 'G', 'Y', 'V', 'Q', 'G', 'C', 'R', 'A', 'L', 'M', 'I', 'T', 'A', 'I', 'L', 'L', 'G', 'F', 'L', 'G', 'L', 'F', 'L', 'G', 'M', 'V', 'G', 'L', 'R', 'A', 'T', 'N', 'V', 'G', 'N', 'M', 'D', 'L', 'S', 'K', 'K', 'A', 'K', 'L', 'L', 'A', 'I', 'A', 'G', 'T', 'L', 'H', 'I', 'L', 'A', 'G', 'A', 'C', 'G', 'M', 'V', 'A', 'I', 'S', 'W', 'Y', 'A', 'V', 'N', 'I', 'T', 'T', 'D', 'F', 'F', 'N', '-', '-', '-', '-', '-', '-', '-', 'P', 'L', 'Y', 'A', 'G', 'T', 'K', 'Y', 'E', 'L', 'G', 'P', 'A', 'L', 'Y', 'L', 'G', 'W', 'S', 'A', 'S', 'L', 'L', 'S', 'I', 'L', 'G', 'G', 'I', 'C', 'V', 'F', 'S', 'T', 'A', 'A', 'A', 'S', 'S', 'K', 'E', 'E', 'P', 'A', 'T', 'R']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.53) self.assertAlmostEqual(alignment.annotations["E-value"], 1.8e-18, places=19) self.assertAlmostEqual(alignment.annotations["Score"], 150.79) self.assertAlmostEqual(alignment.annotations["Identities"], 13) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.177) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 11.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " cHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCcccccCCCccccceEEeccchhhhccCCCCeecccchhHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCceecchHHHHHHHHHHHHHHHHHHHhhhhhcCCCCcccC", ) self.assertEqual(alignment.query.id, "4P79:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:198], "SEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR", ) self.assertEqual( alignment[1], "SEFMSVAVETFGFFMSALGLLMLGLTLSNSYW-----------RVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSML-----------ALSGYVQGCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKYELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~m~~~~l~~~~~~l~~~a~~l~~~a~~t~~W~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~sf~l~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~GLw~~C~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ", ) self.assertEqual(alignment.target.id, "6DLZ_D") self.assertEqual( alignment.target.seq[819:1030], "GLFDRGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSEDETSKKNEEVMTHSGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLCIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLTGGA", ) self.assertEqual(alignment.target.annotations["hmm_name"], "6DLZ_D") self.assertEqual( alignment.target.annotations["hmm_description"], "Glutamate receptor 2,Voltage-dependent calcium channel; Ion channel, TRANSPORT PROTEIN; HET: GLU, CYZ; 3.9A {Rattus norvegicus}; Related PDB entries: 5VHY_B 5WEL_C 5WEL_D 5VHZ_E 5WEK_D 5WEN_C 5VHX_E 5VHY_C 5VHZ_F 5VHY_D 5VHZ_B 5WEN_D 5WEM_C 5WEL_B 5WEM_A 5VHX_C 5WEM_D 5WEK_C 5WEK_A 5VHY_A 5VHW_C 5VHX_A 5VHZ_C 5VHW_D 5VHY_E 5WEN_A 5VHX_B 5VHX_D 5VHW_B 5WEL_A 5VHW_A 5VHZ_D 5WEN_B 5WEK_B 5VHY_F 5VHZ_A 5WEM_B 5WEO_B 5KBT_D 5KBS_A 5KBU_B 5WEO_C 5KBU_A 5KBS_C 5KBU_D 5KBT_A 5KBS_B 5KBT_C 5KBT_B 5KBU_C 5WEO_D 5WEO_A 5KBS_D 6DM2_D 6DLZ_A 6DM0_A 6DM0_B 6DM1_D 6DM2_C 6DM0_C 6DM1_B 6DLZ_B 6DM2_B 6DM1_C 6DM2_A 6DLZ_C 6DM1_A 6DM0_D", ) self.assertEqual( alignment[0], "GLFDRGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSEDETSKKNEEVMTHSGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLCIAASEFY--------KTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLTGGA", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCSTTTHHHHHHHHHHHHHHHHHHHHSCSCSEEEECCSCCCCEEEECSSBCCBCSSSSCSCCCBCCCCCCSSTTTTCHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHTSSTTCSCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCSCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CchHHHHHHHHHHHHHHHHHHHHHHHhccCcceeeccccccccCCcCccccccccccccccceeeeeecCcccCceeecccCCCCcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCceehhhHHHHHHHHHHHHHHHHHHHHHhcCCcccCCCCcccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhcCCC ", ) self.assertEqual( str(alignment), """\ 6DLZ_D 819 GLFDRGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSEDETSKKNEEVMTHS 0 ..|...........................||-----------................. 4P79:A|PD 1 SEFMSVAVETFGFFMSALGLLMLGLTLSNSYW-----------RVSTVHGNVITTNTIFE 6DLZ_D 879 GLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLC 60 .||..|.........|.......-----------.....|.......|....|.|.|... 4P79:A|PD 50 NLWYSCATDSLGVSNCWDFPSML-----------ALSGYVQGCRALMITAILLGFLGLFL 6DLZ_D 939 IAASEFY--------KTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKNS 120 .......--------.........||.....||......|..|......|.......... 4P79:A|PD 99 GMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTK 6DLZ_D 991 YSYGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLTGGA 1030 180 |..|...|.|..........|...........|...... 219 4P79:A|PD 159 YELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR 198 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 819, 851, 862, 902, 913, 946, 946, 1030], [ 1, 33, 33, 73, 73, 106, 114, 198]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'L', 'F', 'D', 'R', 'G', 'V', 'Q', 'M', 'L', 'L', 'T', 'T', 'V', 'G', 'A', 'F', 'A', 'A', 'F', 'S', 'L', 'M', 'T', 'I', 'A', 'V', 'G', 'T', 'D', 'Y', 'W', 'L', 'Y', 'S', 'R', 'G', 'V', 'C', 'K', 'T', 'K', 'S', 'V', 'S', 'E', 'D', 'E', 'T', 'S', 'K', 'K', 'N', 'E', 'E', 'V', 'M', 'T', 'H', 'S', 'G', 'L', 'W', 'R', 'T', 'C', 'C', 'L', 'E', 'G', 'N', 'F', 'K', 'G', 'L', 'C', 'K', 'Q', 'I', 'D', 'H', 'F', 'P', 'E', 'D', 'A', 'D', 'Y', 'E', 'A', 'D', 'T', 'A', 'E', 'Y', 'F', 'L', 'R', 'A', 'V', 'R', 'A', 'S', 'S', 'I', 'F', 'P', 'I', 'L', 'S', 'V', 'I', 'L', 'L', 'F', 'M', 'G', 'G', 'L', 'C', 'I', 'A', 'A', 'S', 'E', 'F', 'Y', '-', '-', '-', '-', '-', '-', '-', '-', 'K', 'T', 'R', 'H', 'N', 'I', 'I', 'L', 'S', 'A', 'G', 'I', 'F', 'F', 'V', 'S', 'A', 'G', 'L', 'S', 'N', 'I', 'I', 'G', 'I', 'I', 'V', 'Y', 'I', 'S', 'A', 'N', 'A', 'G', 'D', 'P', 'S', 'K', 'S', 'D', 'S', 'K', 'K', 'N', 'S', 'Y', 'S', 'Y', 'G', 'W', 'S', 'F', 'Y', 'F', 'G', 'A', 'L', 'S', 'F', 'I', 'I', 'A', 'E', 'M', 'V', 'G', 'V', 'L', 'A', 'V', 'H', 'M', 'F', 'I', 'D', 'R', 'H', 'K', 'Q', 'L', 'T', 'G', 'G', 'A'], ['S', 'E', 'F', 'M', 'S', 'V', 'A', 'V', 'E', 'T', 'F', 'G', 'F', 'F', 'M', 'S', 'A', 'L', 'G', 'L', 'L', 'M', 'L', 'G', 'L', 'T', 'L', 'S', 'N', 'S', 'Y', 'W', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'R', 'V', 'S', 'T', 'V', 'H', 'G', 'N', 'V', 'I', 'T', 'T', 'N', 'T', 'I', 'F', 'E', 'N', 'L', 'W', 'Y', 'S', 'C', 'A', 'T', 'D', 'S', 'L', 'G', 'V', 'S', 'N', 'C', 'W', 'D', 'F', 'P', 'S', 'M', 'L', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'L', 'S', 'G', 'Y', 'V', 'Q', 'G', 'C', 'R', 'A', 'L', 'M', 'I', 'T', 'A', 'I', 'L', 'L', 'G', 'F', 'L', 'G', 'L', 'F', 'L', 'G', 'M', 'V', 'G', 'L', 'R', 'A', 'T', 'N', 'V', 'G', 'N', 'M', 'D', 'L', 'S', 'K', 'K', 'A', 'K', 'L', 'L', 'A', 'I', 'A', 'G', 'T', 'L', 'H', 'I', 'L', 'A', 'G', 'A', 'C', 'G', 'M', 'V', 'A', 'I', 'S', 'W', 'Y', 'A', 'V', 'N', 'I', 'T', 'T', 'D', 'F', 'F', 'N', 'P', 'L', 'Y', 'A', 'G', 'T', 'K', 'Y', 'E', 'L', 'G', 'P', 'A', 'L', 'Y', 'L', 'G', 'W', 'S', 'A', 'S', 'L', 'L', 'S', 'I', 'L', 'G', 'G', 'I', 'C', 'V', 'F', 'S', 'T', 'A', 'A', 'A', 'S', 'S', 'K', 'E', 'E', 'P', 'A', 'T', 'R']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 52.07) self.assertAlmostEqual(alignment.annotations["E-value"], 6.7) self.assertAlmostEqual(alignment.annotations["Score"], 20.51) self.assertAlmostEqual(alignment.annotations["Identities"], 19) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.239) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 3.200) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHHHHhCcCCcccc ", ) self.assertEqual(alignment.query.id, "4P79:A|PDBID|CHAIN|SEQUENCE") self.assertEqual(alignment.query.seq[5:37], "SVAVETFGFFMSALGLLMLGLTLSNSYWRVST") self.assertEqual(alignment[1], "SVAVETFGFFMSALGLLMLGLTLSNS--YWRVST") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~l~~~~~~l~~~a~~l~~~a~~t~~W~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " Rr~lval~~fl~vLallIHfiLLST~~~NWl~~~", ) self.assertEqual(alignment.target.id, "5YQ7_F") self.assertEqual( alignment.target.seq[8:42], "RTSVVVSTLLGLVMALLIHFVVLSSGAFNWLRAP" ) self.assertEqual(alignment.target.annotations["hmm_name"], "5YQ7_F") self.assertEqual( alignment.target.annotations["hmm_description"], "Beta subunit of light-harvesting 1; Photosynthetic core complex, PHOTOSYNTHESIS; HET: MQE, BCL, HEM, KGD, BPH;{Roseiflexus castenholzii}; Related PDB entries: 5YQ7_V 5YQ7_3 5YQ7_T 5YQ7_J 5YQ7_9 5YQ7_N 5YQ7_A 5YQ7_P 5YQ7_H 5YQ7_D 5YQ7_5 5YQ7_7 5YQ7_1 5YQ7_R", ) self.assertEqual(alignment[0], "RTSVVVSTLLGLVMALLIHFVVLSSGAFNWLRAP") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHCCCCCTTSSSCCSCC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHHHHcccccccccCC", ) self.assertEqual( str(alignment), """\ 5YQ7_F 8 RTSVVVSTLLGLVMALLIHFVVLSSGAFNWLRAP 42 0 ...|...........||.....||..--.|.... 34 4P79:A|PD 5 SVAVETFGFFMSALGLLMLGLTLSNS--YWRVST 37 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 8, 34, 36, 42], [ 5, 31, 31, 37]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'T', 'S', 'V', 'V', 'V', 'S', 'T', 'L', 'L', 'G', 'L', 'V', 'M', 'A', 'L', 'L', 'I', 'H', 'F', 'V', 'V', 'L', 'S', 'S', 'G', 'A', 'F', 'N', 'W', 'L', 'R', 'A', 'P'], ['S', 'V', 'A', 'V', 'E', 'T', 'F', 'G', 'F', 'F', 'M', 'S', 'A', 'L', 'G', 'L', 'L', 'M', 'L', 'G', 'L', 'T', 'L', 'S', 'N', 'S', '-', '-', 'Y', 'W', 'R', 'V', 'S', 'T']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_length(self): """Test getting the number of alignments without parsing the file.""" stream = open(self.path) alignments = Align.parse(stream, "hhr") stream.close() self.assertEqual(len(alignments), 8) class Align_hhr_4y9h_hhsearch_server_NOssm(unittest.TestCase): path = os.path.join("HHsuite", "4y9h_hhsearch_server_NOssm.hhr") def test_reading(self): alignments = Align.parse(self.path, "hhr") self.assertEqual(alignments.metadata["No_of_seqs"], (141, 1242)) self.assertAlmostEqual(alignments.metadata["Neff"], 8.55177) self.assertEqual(alignments.metadata["Searched_HMMs"], 46616) self.assertEqual(alignments.metadata["Rundate"], "Thu Nov 29 16:28:55 2018") self.assertEqual( alignments.metadata["Command line"], "hhsearch -cpu 8 -i ../results/full.a3m -d /cluster/toolkit/production/databases/hh-suite/mmcif70/pdb70 -o ../results/4Y9H_1.hhr -oa3m ../results/4Y9H_1.a3m -p 50 -Z 250 -loc -z 1 -b 1 -B 250 -ssm 0 -sc 1 -seq 1 -dbstrlen 10000 -norealign -maxres 32000 -contxt /cluster/toolkit/production/bioprogs/tools/hh-suite-build/data/context_data.crf", ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 2.1e-48, places=49) self.assertAlmostEqual(alignment.annotations["Score"], 320.44) self.assertAlmostEqual(alignment.annotations["Identities"], 100) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.574) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.500) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhhC", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:226], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment[1], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~va~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~~~~~~~mi~~g~~g~~~~~~~~~w~~~~~s~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~i~y~ilDi~~K~~f~~~l~~~~~~~~ ", ) self.assertEqual(alignment.target.id, "5ZIM_A") self.assertEqual( alignment.target.seq[1:227], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual(alignment.target.annotations["hmm_name"], "5ZIM_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Bacteriorhodopsin; proton pump, membrane protein, PROTON; HET: L2P, RET; 1.25A {Halobacterium salinarum}; Related PDB entries: 1R84_A 1KG8_A 1KME_B 1KGB_A 1KG9_A 1KME_A 4X31_A 5ZIL_A 1E0P_A 4X32_A 5ZIN_A 1S53_B 1S51_B 1S53_A 1S54_A 1F50_A 1S54_B 1S51_A 1F4Z_A 5J7A_A 1S52_B 1S52_A 4Y9H_A 3T45_A 3T45_C 3T45_B 1C3W_A 1L0M_A", ) self.assertEqual( alignment[0], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSTTHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEEEEETTEEEEEETHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHHHSCTTSSSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCCSCHHHHHHHHHHHHCCCCCCHHHHHHTSGGGSC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHcCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhC ", ) self.assertEqual( str(alignment), """\ 5ZIM_A 1 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 4Y9H:A|PD 0 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG 5ZIM_A 61 LTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVG 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 4Y9H:A|PD 60 LTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVG 5ZIM_A 121 ALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAY 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 4Y9H:A|PD 120 ALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAY 5ZIM_A 181 PVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 227 180 |||||||||||||||||||||||||||||||||||||||||||||| 226 4Y9H:A|PD 180 PVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 226 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 227], [ 0, 226]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F', 'G'], ['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 2.9e-45, places=46) self.assertAlmostEqual(alignment.annotations["Score"], 307.43) self.assertAlmostEqual(alignment.annotations["Identities"], 100) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.574) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.700) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhhC", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:226], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment[1], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~~~~~~~~m~~~~l~f~~~~~~~~~~~~r~~~~l~~~i~~iaa~~Y~~ma~g~g~~~~~~~~~~r~v~~~RYvdW~iTtPlll~~l~~la~~~~~~~~~~v~~~~~mi~~G~~g~~~~~~~~kw~~~~~s~~~f~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~eg~~~is~~~e~i~y~ilDv~~K~~f~~~ll~~~~~~~ ", ) self.assertEqual(alignment.target.id, "1M0K_A") self.assertEqual( alignment.target.seq[18:244], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1M0K_A") self.assertEqual( alignment.target.annotations["hmm_description"], "BACTERIORHODOPSIN; ION PUMP, MEMBRANE PROTEIN, RETINAL; HET: RET, SQU, LI1; 1.43A {Halobacterium salinarum} SCOP: f.13.1.1; Related PDB entries: 4XXJ_B 4XXJ_A 4XXJ_C 6G7L_A 5VN7_B 1M0M_A 4HWL_A 2ZFE_A 4FPD_A 6G7J_A 3VHZ_A 1M0L_A 2ZZL_A 4HYX_A 4HWL_B 4HYX_B 6G7K_A 6G7I_A 3VI0_A 5VN7_A 5VN9_B 5VN9_A 3COC_B 2I21_A 5B34_A 3HAQ_A 1S8L_A 1TN0_B 1O0A_A 1JV6_A 1TN0_A 5BR2_A 2I1X_A 1UCQ_A 1MGY_A 1C8R_A 3HAR_A 1P8U_A 3UTX_A 1Q5I_A 1Q5J_A 1Q5J_B 1JV7_A 1P8I_A 1S8J_A 3COC_A 3HAO_A 1PY6_B 1PXR_B 1Q5I_B 3UTY_A 2NTU_A 1PXS_B 5BR5_A 1PXS_A 3HAS_A 1PXR_A 1TN5_A 2WJL_A 3HAP_A 3COD_A 1TN5_B 3HAO_B 2I20_A 2WJK_A 1R2N_A 3UTV_A 3UTX_B 3HAN_A 1PY6_A 1VJM_A 3UTY_B 5B35_A 3COD_B 3UTW_A 2NTW_A 4OV0_A 1P8H_A 1CWQ_A 6G7H_A 5H2J_A 1BRD_A 5H2H_A 1X0I_1 5A44_A 1QM8_A 1X0S_A 5B6V_A 1BM1_A 1AP9_A 2BRD_A 1IW6_A 3MBV_A 5H2P_A 1QKP_A 5H2O_A 5H2N_A 5B6X_A 1FBB_A 1CWQ_B 4MD2_A 1QKO_A 1IW9_A 1QHJ_A 1AT9_A 1DZE_A 4MD1_A 5H2K_A 1X0K_1 5B6Z_A 5H2L_A 5H2I_A 1FBK_A 1IXF_A 3NS0_A 1BRX_A 3NSB_A 5H2M_A 2AT9_A 5B6Y_A 5B6W_A 5A45_A 1XJI_A 1BRR_B 1BRR_A 1BRR_C", ) self.assertEqual( alignment[0], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSTTHHHHHHHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTTTCEEEEETTEEEEECTHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCCSCHHHHHHHHHHHHHCCCCCHHHHHHHSGGGCC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CchHHHHHHHHHHHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHHHHHHHHHHHHHcCCCceeccCCCCcCccchHHHHHHHhHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHcccchhhHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc ", ) self.assertEqual( str(alignment), """\ 1M0K_A 18 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 4Y9H:A|PD 0 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG 1M0K_A 78 LTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVG 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 4Y9H:A|PD 60 LTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVG 1M0K_A 138 ALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAY 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 4Y9H:A|PD 120 ALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAY 1M0K_A 198 PVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 244 180 |||||||||||||||||||||||||||||||||||||||||||||| 226 4Y9H:A|PD 180 PVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 226 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 18, 244], [ 0, 226]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F', 'G'], ['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 4.4e-43, places=44) self.assertAlmostEqual(alignment.annotations["Score"], 291.03) self.assertAlmostEqual(alignment.annotations["Identities"], 55) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.956) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.200) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhhC", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:226], "RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment[1], "RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEG-AGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~lw~~~~~~~~~~~~f~~~~~~~~~~~~R~~~~l~~~i~~va~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~iTtPlll~~l~~lag~~~~~~~~~~~~~~~mi~~G~~g~~~~~~~~~w~~~~~s~~~~~~i~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~~i~~~~~~i~~~vlDv~~K~~fg~~l~~~~~~~~ ", ) self.assertEqual(alignment.target.id, "4FBZ_A") self.assertEqual( alignment.target.seq[5:231], "GPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMQEFYIITTFITTIAAAMYFAMATGFGVTEVVVGDEALTIYWARYADWLFTTPLLLLDLGLLAGANRNTIATLIGLDVFMIGTGMIAAFAATPGTRIAWWGISTGALLALLYVLVGTLSKDARGQSPEVASLFGRLRNLVIVLWLLYPVVWILGTEGTFGILPLYWETAAFMVLDLSAKVGFGVVLLRSRSVLR", ) self.assertEqual(alignment.target.annotations["hmm_name"], "4FBZ_A") self.assertEqual( alignment.target.annotations["hmm_description"], "deltarhodopsin; 7 transmembrane helices, light-driven proton; HET: RET, L2P, 22B, SQL, BNG, SO4; 2.7A {Haloterrigena thermotolerans} SCOP: f.13.1.0", ) self.assertEqual( alignment[0], "GPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMQEFYIITTFITTIAAAMYFAMATGFGVTEVVVGDEALTIYWARYADWLFTTPLLLLDLGLLAGANRNTIATLIGLDVFMIGTGMIAAFAATPGTRIAWWGISTGALLALLYVLVGTLSKDARGQSPEVASLFGRLRNLVIVLWLLYPVVWILGTEGTFGILPLYWETAAFMVLDLSAKVGFGVVLLRSRSVLR", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CTTHHHHHHHHHHHHHHHHHHHHHTTTCCSTTHHHHHHHHHHHHHHHHHHHHHHHTTTTCEEEECSSCEEEECTHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGSSCCSCHHHHHHHHHHHHHCCCCCHHHHHSSCHHHHG ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " hhHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHHHHHHcCCCceeEecCCcceeeeHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccCCCCChHHHHHHHHHHHHHHHHhHHHHHHHhhHHHH ", ) self.assertEqual( str(alignment), """\ 4FBZ_A 5 GPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMQEFYIITTFITTIAAAMYFAMATGFGV 0 .||.|||..||..|.||||||...|.||.|.....||.|||....||..||..|..|.|. 4Y9H:A|PD 1 RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGL 4FBZ_A 65 TEVVVGDEALTIYWARYADWLFTTPLLLLDLGLLAGANRNTIATLIGLDVFMIGTGMIAA 60 |.|..|.|...||||||||||||||||||||.||..|...||..|.|.|..|||||...| 4Y9H:A|PD 61 TMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGA 4FBZ_A 125 FAATPGTRIAWWGISTGALLALLYVLVGTLSKDARGQSPEVASLFGRLRNLVIVLWLLYP 120 .......|..||.|||.|.|..||||.......|....|||||.|..|||...|||..|| 4Y9H:A|PD 121 LTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYP 4FBZ_A 185 VVWILGTEGTFGILPLYWETAAFMVLDLSAKVGFGVVLLRSRSVLR 231 180 |||..|.||-.||.||..||..|||||.|||||||..|||||.... 226 4Y9H:A|PD 181 VVWLIGSEG-AGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 226 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 5, 194, 195, 231], [ 1, 190, 190, 226]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'P', 'E', 'S', 'I', 'W', 'L', 'W', 'I', 'G', 'T', 'I', 'G', 'M', 'T', 'L', 'G', 'T', 'L', 'Y', 'F', 'V', 'G', 'R', 'G', 'R', 'G', 'V', 'R', 'D', 'R', 'K', 'M', 'Q', 'E', 'F', 'Y', 'I', 'I', 'T', 'T', 'F', 'I', 'T', 'T', 'I', 'A', 'A', 'A', 'M', 'Y', 'F', 'A', 'M', 'A', 'T', 'G', 'F', 'G', 'V', 'T', 'E', 'V', 'V', 'V', 'G', 'D', 'E', 'A', 'L', 'T', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'G', 'L', 'L', 'A', 'G', 'A', 'N', 'R', 'N', 'T', 'I', 'A', 'T', 'L', 'I', 'G', 'L', 'D', 'V', 'F', 'M', 'I', 'G', 'T', 'G', 'M', 'I', 'A', 'A', 'F', 'A', 'A', 'T', 'P', 'G', 'T', 'R', 'I', 'A', 'W', 'W', 'G', 'I', 'S', 'T', 'G', 'A', 'L', 'L', 'A', 'L', 'L', 'Y', 'V', 'L', 'V', 'G', 'T', 'L', 'S', 'K', 'D', 'A', 'R', 'G', 'Q', 'S', 'P', 'E', 'V', 'A', 'S', 'L', 'F', 'G', 'R', 'L', 'R', 'N', 'L', 'V', 'I', 'V', 'L', 'W', 'L', 'L', 'Y', 'P', 'V', 'V', 'W', 'I', 'L', 'G', 'T', 'E', 'G', 'T', 'F', 'G', 'I', 'L', 'P', 'L', 'Y', 'W', 'E', 'T', 'A', 'A', 'F', 'M', 'V', 'L', 'D', 'L', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'V', 'V', 'L', 'L', 'R', 'S', 'R', 'S', 'V', 'L', 'R'], ['R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', '-', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 1e-42, places=43) self.assertAlmostEqual(alignment.annotations["Score"], 291.62) self.assertAlmostEqual(alignment.annotations["Identities"], 57) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.005) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.800) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhhC", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:226], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment[1], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVP-FGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~vaa~~Y~~ma~g~g~~~~~~~~~~~r~v~~~RYv~W~iTtPlll~~l~~la~~~~~~~~~~v~~~~~Mi~~G~~g~~~~~~~~~~~~~~~g~~~f~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPivw~l~~~g~~~i~~~~e~i~~~ilDv~~K~~f~~~l~~~~~~~~ ", ) self.assertEqual(alignment.target.id, "3WQJ_A") self.assertEqual( alignment.target.seq[15:242], "GRPETLWLGIGTLLMLIGTFYFIARGWGVTDKEAREYYAITILVPGIASAAYLAMFFGIGVTEVELASGTVLDIYYARYADWLFTTPLLLLDLALLAKVDRVTIGTLIGVDALMIVTGLIGALSKTPLARYTWWLFSTIAFLFVLYYLLTSLRSAAAKRSEEVRSTFNTLTALVAVLWTAYPILWIVGTEGAGVVGLGIETLAFMVLDVTAKVGFGFVLLRSRAILG", ) self.assertEqual(alignment.target.annotations["hmm_name"], "3WQJ_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Archaerhodopsin-2; 7 trans-membrane helices, light-driven proton; HET: RET, L3P, L2P, 22B, SQL, L4P; 1.8A {Halobacterium}; Related PDB entries: 2Z55_B 2EI4_A 2Z55_D 1VGO_A 2Z55_E 1VGO_B 2Z55_A 1UAZ_A 1UAZ_B", ) self.assertEqual( alignment[0], "GRPETLWLGIGTLLMLIGTFYFIARGWGVTDKEAREYYAITILVPGIASAAYLAMFFGIGVTEVELASGTVLDIYYARYADWLFTTPLLLLDLALLAKVDRVTIGTLIGVDALMIVTGLIGALSKTPLARYTWWLFSTIAFLFVLYYLLTSLRSAAAKRSEEVRSTFNTLTALVAVLWTAYPILWIVGTEGAGVVGLGIETLAFMVLDVTAKVGFGFVLLRSRAILG", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " SCTTHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHSTTCEEEECTTSCEEEECTHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCCSCHHHHHHHHHHHHHCCCCCHHHHHHTCTTC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CchHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHcCCCceeEecCCCCeeeecHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc ", ) self.assertEqual( str(alignment), """\ 3WQJ_A 15 GRPETLWLGIGTLLMLIGTFYFIARGWGVTDKEAREYYAITILVPGIASAAYLAMFFGIG 0 ||||..||..||.||..||.||...|.||.|..|...||||.|||.||...||.|..|.| 4Y9H:A|PD 0 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG 3WQJ_A 75 VTEVELASGTVLDIYYARYADWLFTTPLLLLDLALLAKVDRVTIGTLIGVDALMIVTGLI 60 .|.|.-..|....||.||||||||||||||||||||...|..||..|.|.|..||.|||. 4Y9H:A|PD 60 LTMVP-FGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLV 3WQJ_A 135 GALSKTPLARYTWWLFSTIAFLFVLYYLLTSLRSAAAKRSEEVRSTFNTLTALVAVLWTA 120 |||.|....|..||..||.|.|..||.|.....|.|.....||.|||..|.....|||.| 4Y9H:A|PD 119 GALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSA 3WQJ_A 195 YPILWIVGTEGAGVVGLGIETLAFMVLDVTAKVGFGFVLLRSRAILG 242 180 ||..|..|.||||.|.|.||||.||||||.||||||..|||||||.| 227 4Y9H:A|PD 179 YPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 226 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 15, 80, 81, 242], [ 0, 65, 65, 226]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'R', 'P', 'E', 'T', 'L', 'W', 'L', 'G', 'I', 'G', 'T', 'L', 'L', 'M', 'L', 'I', 'G', 'T', 'F', 'Y', 'F', 'I', 'A', 'R', 'G', 'W', 'G', 'V', 'T', 'D', 'K', 'E', 'A', 'R', 'E', 'Y', 'Y', 'A', 'I', 'T', 'I', 'L', 'V', 'P', 'G', 'I', 'A', 'S', 'A', 'A', 'Y', 'L', 'A', 'M', 'F', 'F', 'G', 'I', 'G', 'V', 'T', 'E', 'V', 'E', 'L', 'A', 'S', 'G', 'T', 'V', 'L', 'D', 'I', 'Y', 'Y', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'A', 'K', 'V', 'D', 'R', 'V', 'T', 'I', 'G', 'T', 'L', 'I', 'G', 'V', 'D', 'A', 'L', 'M', 'I', 'V', 'T', 'G', 'L', 'I', 'G', 'A', 'L', 'S', 'K', 'T', 'P', 'L', 'A', 'R', 'Y', 'T', 'W', 'W', 'L', 'F', 'S', 'T', 'I', 'A', 'F', 'L', 'F', 'V', 'L', 'Y', 'Y', 'L', 'L', 'T', 'S', 'L', 'R', 'S', 'A', 'A', 'A', 'K', 'R', 'S', 'E', 'E', 'V', 'R', 'S', 'T', 'F', 'N', 'T', 'L', 'T', 'A', 'L', 'V', 'A', 'V', 'L', 'W', 'T', 'A', 'Y', 'P', 'I', 'L', 'W', 'I', 'V', 'G', 'T', 'E', 'G', 'A', 'G', 'V', 'V', 'G', 'L', 'G', 'I', 'E', 'T', 'L', 'A', 'F', 'M', 'V', 'L', 'D', 'V', 'T', 'A', 'K', 'V', 'G', 'F', 'G', 'F', 'V', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'L', 'G'], ['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', '-', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 1.3e-42, places=43) self.assertAlmostEqual(alignment.annotations["Score"], 289.73) self.assertAlmostEqual(alignment.annotations["Identities"], 55) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.964) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.100) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:225], "RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIF", ) self.assertEqual( alignment[1], "RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKV------YSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIF", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~lw~~~~~~~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~va~~~Y~~ma~~~g~~~~~~~~~~r~v~~~RYv~W~ittPlll~~l~~lag~~~~~~~~~~~~~~~mi~~g~~~~~~~~~~~~~~~~~~w~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~~~ilDv~~K~~f~~~ll~~~~~~ ", ) self.assertEqual(alignment.target.id, "4L35_A") self.assertEqual( alignment.target.seq[4:234], "EGEAIWLWLGTAGMFLGMLYFIARGWGETDSRRQKFYIATILITAIAFVNYLAMALGFGLTIVEIAGEQRPIYWARYSDWLFTTPLLLYDLGLLAGADRNTISSLVSLDVLMIGTGLVATLSAGSGVLSAGAERLVWWGISTAFLLVLLYFLFSSLSGRVADLPSDTRSTFKTLRNLVTVVWLVYPVWWLVGTEGIGLVGIGIETAGFMVIDLVAKVGFGIILLRSHGVL", ) self.assertEqual(alignment.target.annotations["hmm_name"], "4L35_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Cruxrhodopsin-3; protein-bacterioruberin complex, seven transmembrane alpha; HET: RET, 22B; 2.1A {Haloarcula vallismortis} SCOP: f.13.1.0; Related PDB entries: 4PXK_A 4JR8_A", ) self.assertEqual( alignment[0], "EGEAIWLWLGTAGMFLGMLYFIARGWGETDSRRQKFYIATILITAIAFVNYLAMALGFGLTIVEIAGEQRPIYWARYSDWLFTTPLLLYDLGLLAGADRNTISSLVSLDVLMIGTGLVATLSAGSGVLSAGAERLVWWGISTAFLLVLLYFLFSSLSGRVADLPSDTRSTFKTLRNLVTVVWLVYPVWWLVGTEGIGLVGIGIETAGFMVIDLVAKVGFGIILLRSHGVL", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSSHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEEEEETTEEEEEETHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCCCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCSSCHHHHHHHHHHHHHCCCCCHHHHHTSCHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " hhHHHHHHHHHHHHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHHHHHHHHHHcCCCeeEeecCCcceeeeHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHcccCCccCcchHHHHHHHHHHHHHHHHHHHHHhhhhHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHcchh ", ) self.assertEqual( str(alignment), """\ 4L35_A 4 EGEAIWLWLGTAGMFLGMLYFIARGWGETDSRRQKFYIATILITAIAFVNYLAMALGFGL 0 ..|.|||.||||.|.||.|||...|.|..|....|||..|.|..||||..||.|.||.|| 4Y9H:A|PD 1 RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGL 4L35_A 64 TIVEIAGEQRPIYWARYSDWLFTTPLLLYDLGLLAGADRNTISSLVSLDVLMIGTGLVAT 60 |.|...|||.|||||||.||||||||||.||.||..||..||..||..|..|||||||.. 4Y9H:A|PD 61 TMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGA 4L35_A 124 LSAGSGVLSAGAERLVWWGISTAFLLVLLYFLFSSLSGRVADLPSDTRSTFKTLRNLVTV 120 |...------...|.|||.||||..|..||.||...............||||.|||...| 4Y9H:A|PD 121 LTKV------YSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVV 4L35_A 184 VWLVYPVWWLVGTEGIGLVGIGIETAGFMVIDLVAKVGFGIILLRSHGVL 234 180 .|..|||.||.|.||.|.|...|||..|||.|..||||||.|||||.... 230 4Y9H:A|PD 175 LWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIF 225 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 4, 128, 134, 234], [ 1, 125, 125, 225]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'G', 'E', 'A', 'I', 'W', 'L', 'W', 'L', 'G', 'T', 'A', 'G', 'M', 'F', 'L', 'G', 'M', 'L', 'Y', 'F', 'I', 'A', 'R', 'G', 'W', 'G', 'E', 'T', 'D', 'S', 'R', 'R', 'Q', 'K', 'F', 'Y', 'I', 'A', 'T', 'I', 'L', 'I', 'T', 'A', 'I', 'A', 'F', 'V', 'N', 'Y', 'L', 'A', 'M', 'A', 'L', 'G', 'F', 'G', 'L', 'T', 'I', 'V', 'E', 'I', 'A', 'G', 'E', 'Q', 'R', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'S', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'Y', 'D', 'L', 'G', 'L', 'L', 'A', 'G', 'A', 'D', 'R', 'N', 'T', 'I', 'S', 'S', 'L', 'V', 'S', 'L', 'D', 'V', 'L', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'A', 'T', 'L', 'S', 'A', 'G', 'S', 'G', 'V', 'L', 'S', 'A', 'G', 'A', 'E', 'R', 'L', 'V', 'W', 'W', 'G', 'I', 'S', 'T', 'A', 'F', 'L', 'L', 'V', 'L', 'L', 'Y', 'F', 'L', 'F', 'S', 'S', 'L', 'S', 'G', 'R', 'V', 'A', 'D', 'L', 'P', 'S', 'D', 'T', 'R', 'S', 'T', 'F', 'K', 'T', 'L', 'R', 'N', 'L', 'V', 'T', 'V', 'V', 'W', 'L', 'V', 'Y', 'P', 'V', 'W', 'W', 'L', 'V', 'G', 'T', 'E', 'G', 'I', 'G', 'L', 'V', 'G', 'I', 'G', 'I', 'E', 'T', 'A', 'G', 'F', 'M', 'V', 'I', 'D', 'L', 'V', 'A', 'K', 'V', 'G', 'F', 'G', 'I', 'I', 'L', 'L', 'R', 'S', 'H', 'G', 'V', 'L'], ['R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', '-', '-', '-', '-', '-', '-', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 2.2e-42, places=43) self.assertAlmostEqual(alignment.annotations["Score"], 289.87) self.assertAlmostEqual(alignment.annotations["Identities"], 56) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.948) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhhC", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:226], "RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment[1], "RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPF-GGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~~~~~~~m~~~~l~f~~~~~~~~~~~~r~~~~l~~~i~~vaa~~Y~~ma~g~g~~~~~~~~g~~r~v~~~RYv~W~iTtPlll~~l~llag~~~~~~~~~i~~~~~Mi~~G~~g~~~~~~~~~w~~~~is~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~L~~~~~v~W~~YPivw~l~~~G~~~is~~~e~i~~~vlDil~K~~fg~~ll~~~~~~~ ", ) self.assertEqual(alignment.target.id, "4QI1_A") self.assertEqual( alignment.target.seq[13:239], "EGEGIWLALGTIGMLLGMLYFIADGLDVQDPRQKEFYVITILIPAIAAASYLSMFFGFGLTEVSLANGRVVDVYWARYADWLFTTPLLLLDIGLLAGASQRDIGALVGIDAFMIVTGLVATLTKVVVARYAFWTISTISMVFLLYYLVAVFGEAVSDADEDTRSTFNALRNIILVTWAIYPVAWLVGTEGLALTGLYGETLLFMVLDLVAKVGFGFILLRSRAIMG", ) self.assertEqual(alignment.target.annotations["hmm_name"], "4QI1_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Bacteriorhodopsin-I; Bacteriorhodopsin, proton pump, Membrane, MEMBRANE; HET: MPG, RET; 1.85A {Haloquadratum walsbyi} SCOP: f.13.1.0; Related PDB entries: 5ITC_A 5KKH_A 5ITE_B 5KKH_C 5ITE_C 5ITC_C 5ITC_B 5KKH_B 5ITE_A 4QI1_B 4WAV_B 4WAV_A 4QID_B 4QID_A 4QI1_C", ) self.assertEqual( alignment[0], "EGEGIWLALGTIGMLLGMLYFIADGLDVQDPRQKEFYVITILIPAIAAASYLSMFFGFGLTEVSLANGRVVDVYWARYADWLFTTPLLLLDIGLLAGASQRDIGALVGIDAFMIVTGLVATLTKVVVARYAFWTISTISMVFLLYYLVAVFGEAVSDADEDTRSTFNALRNIILVTWAIYPVAWLVGTEGLALTGLYGETLLFMVLDLVAKVGFGFILLRSRAIMG", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " SSTHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEEEECTTSCEEEEETHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCSSCHHHHHHHHHHHHCCCCCCHHHHHHTCGGGC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " hhHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHHHHHHHHHHHHHcCCCceeeeccCCCeeeeeHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC ", ) self.assertEqual( str(alignment), """\ 4QI1_A 13 EGEGIWLALGTIGMLLGMLYFIADGLDVQDPRQKEFYVITILIPAIAAASYLSMFFGFGL 0 ..|.|||||||..|.||.|||...|..|.||..|.||.||.|.||||...||||..|.|| 4Y9H:A|PD 1 RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGL 4QI1_A 73 TEVSLANGRVVDVYWARYADWLFTTPLLLLDIGLLAGASQRDIGALVGIDAFMIVTGLVA 60 |.|..-.|.....||||||||||||||||||..||..|.|..|.||||.|..||.||||. 4Y9H:A|PD 61 TMVPF-GGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVG 4QI1_A 133 TLTKVVVARYAFWTISTISMVFLLYYLVAVFGEAVSDADEDTRSTFNALRNIILVTWAIY 120 .||||...|...|.|||..|...||.|...|............|||..|||...|.|..| 4Y9H:A|PD 120 ALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAY 4QI1_A 193 PVAWLVGTEGLALTGLYGETLLFMVLDLVAKVGFGFILLRSRAIMG 239 180 ||.||.|.||.....|..|||||||||..||||||.||||||||.| 226 4Y9H:A|PD 180 PVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 226 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 13, 78, 79, 239], [ 1, 66, 66, 226]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'G', 'E', 'G', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'I', 'G', 'M', 'L', 'L', 'G', 'M', 'L', 'Y', 'F', 'I', 'A', 'D', 'G', 'L', 'D', 'V', 'Q', 'D', 'P', 'R', 'Q', 'K', 'E', 'F', 'Y', 'V', 'I', 'T', 'I', 'L', 'I', 'P', 'A', 'I', 'A', 'A', 'A', 'S', 'Y', 'L', 'S', 'M', 'F', 'F', 'G', 'F', 'G', 'L', 'T', 'E', 'V', 'S', 'L', 'A', 'N', 'G', 'R', 'V', 'V', 'D', 'V', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'I', 'G', 'L', 'L', 'A', 'G', 'A', 'S', 'Q', 'R', 'D', 'I', 'G', 'A', 'L', 'V', 'G', 'I', 'D', 'A', 'F', 'M', 'I', 'V', 'T', 'G', 'L', 'V', 'A', 'T', 'L', 'T', 'K', 'V', 'V', 'V', 'A', 'R', 'Y', 'A', 'F', 'W', 'T', 'I', 'S', 'T', 'I', 'S', 'M', 'V', 'F', 'L', 'L', 'Y', 'Y', 'L', 'V', 'A', 'V', 'F', 'G', 'E', 'A', 'V', 'S', 'D', 'A', 'D', 'E', 'D', 'T', 'R', 'S', 'T', 'F', 'N', 'A', 'L', 'R', 'N', 'I', 'I', 'L', 'V', 'T', 'W', 'A', 'I', 'Y', 'P', 'V', 'A', 'W', 'L', 'V', 'G', 'T', 'E', 'G', 'L', 'A', 'L', 'T', 'G', 'L', 'Y', 'G', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'L', 'V', 'A', 'K', 'V', 'G', 'F', 'G', 'F', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'M', 'G'], ['R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', '-', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 4.4e-42, places=43) self.assertAlmostEqual(alignment.annotations["Score"], 282.32) self.assertAlmostEqual(alignment.annotations["Identities"], 29) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.533) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.300) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:224], "RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~w~~~~~~~~~~~~f~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~RY~~W~vTtPlll~~l~~lag~~~~~~~~~i~~~~~mi~~G~~~~~~~~~~~~~~~~i~~~~~~~i~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~yPi~w~l~~~g~~~i~~~~e~~~~~~~Di~~K~~f~~~l~~~~~~ ", ) self.assertEqual(alignment.target.id, "1H2S_A") self.assertEqual( alignment.target.seq[1:218], "VGLTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYVVMALGVGWVPVAERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAAT", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1H2S_A") self.assertEqual( alignment.target.annotations["hmm_description"], "SENSORY RHODOPSIN II, SENSORY RHODOPSIN; MEMBRANE PROTEIN, MENBRANE PROTEIN COMPLEX; HET: BOG, RET; 1.93A {NATRONOMONAS PHARAONIS} SCOP: f.13.1.1; Related PDB entries: 1JGJ_A", ) self.assertEqual( alignment[0], "VGLTTLFWLGAIGMLVGTLAFAWAGRDAG-SGERRYYVTLVGISGIAAVAYVVMALGVGWVPV----AERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPG-IERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAAT", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CSHHHHHHHHHHHHHHHHHHHHHHTTTCCTTTHHHHHHHHHHHHHHHHHHHHHHTTCSEECCTTSCEEHHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTSCHHHHHHHHHHHHHHHHHHTTHHHHHHHSTTTTCCSCHHHHHHHHHHHHCCCCCCHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " chHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCccccCcccccHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHHHHHHhCCcchHHHHHHHHHHHHHHHHHHHHchHHHHHhhcchhHHHHHHHHHHHHHHHHHHHHHHHHHCccccCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 1H2S_A 1 VGLTTLFWLGAIGMLVGTLAFAWAGRDAG-SGERRYYVTLVGISGIAAVAYVVMALGVGW 0 ........||...|..|||.|...|....-......|........||...|..|.||.|. 4Y9H:A|PD 1 RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGL 1H2S_A 60 VPV----AERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGA 60 ..|----........||.||..||||....|.||...|.................|..|| 4Y9H:A|PD 61 TMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGA 1H2S_A 116 MVPG-IERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYP 120 ....-..|.........|.|...|.|....|..|........|....|||.||.||..|| 4Y9H:A|PD 121 LTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYP 1H2S_A 175 FIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAAT 218 180 ..||.|..|...........|...||...|||||.|.|...|. 223 4Y9H:A|PD 181 VVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 30, 30, 63, 63, 120, 120, 218], [ 1, 30, 31, 64, 68, 125, 126, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['V', 'G', 'L', 'T', 'T', 'L', 'F', 'W', 'L', 'G', 'A', 'I', 'G', 'M', 'L', 'V', 'G', 'T', 'L', 'A', 'F', 'A', 'W', 'A', 'G', 'R', 'D', 'A', 'G', '-', 'S', 'G', 'E', 'R', 'R', 'Y', 'Y', 'V', 'T', 'L', 'V', 'G', 'I', 'S', 'G', 'I', 'A', 'A', 'V', 'A', 'Y', 'V', 'V', 'M', 'A', 'L', 'G', 'V', 'G', 'W', 'V', 'P', 'V', '-', '-', '-', '-', 'A', 'E', 'R', 'T', 'V', 'F', 'A', 'P', 'R', 'Y', 'I', 'D', 'W', 'I', 'L', 'T', 'T', 'P', 'L', 'I', 'V', 'Y', 'F', 'L', 'G', 'L', 'L', 'A', 'G', 'L', 'D', 'S', 'R', 'E', 'F', 'G', 'I', 'V', 'I', 'T', 'L', 'N', 'T', 'V', 'V', 'M', 'L', 'A', 'G', 'F', 'A', 'G', 'A', 'M', 'V', 'P', 'G', '-', 'I', 'E', 'R', 'Y', 'A', 'L', 'F', 'G', 'M', 'G', 'A', 'V', 'A', 'F', 'L', 'G', 'L', 'V', 'Y', 'Y', 'L', 'V', 'G', 'P', 'M', 'T', 'E', 'S', 'A', 'S', 'Q', 'R', 'S', 'S', 'G', 'I', 'K', 'S', 'L', 'Y', 'V', 'R', 'L', 'R', 'N', 'L', 'T', 'V', 'I', 'L', 'W', 'A', 'I', 'Y', 'P', 'F', 'I', 'W', 'L', 'L', 'G', 'P', 'P', 'G', 'V', 'A', 'L', 'L', 'T', 'P', 'T', 'V', 'D', 'V', 'A', 'L', 'I', 'V', 'Y', 'L', 'D', 'L', 'V', 'T', 'K', 'V', 'G', 'F', 'G', 'F', 'I', 'A', 'L', 'D', 'A', 'A', 'A', 'T'], ['R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 4.6e-42, places=43) self.assertAlmostEqual(alignment.annotations["Score"], 282.87) self.assertAlmostEqual(alignment.annotations["Identities"], 29) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.443) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.400) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:225], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIF", ) self.assertEqual( alignment[1], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIF", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~g~~~lw~~~~~~~~~~~~f~~~~~r~~~~~R~~~~l~~~i~~va~~~Y~~ma~~~~~~~~~~~r~v~~~RYv~W~vTtPlll~~l~~l~g~~~~~~~~~v~~~~~mi~~g~~~~~~~~~~~~w~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~v~W~~YPivw~l~~g~~~i~~~~e~i~~~vlDv~~K~~f~~~ll~~~~~~ ", ) self.assertEqual(alignment.target.id, "3AM6_A") self.assertEqual( alignment.target.seq[5:225], "TETGMIAQWIVFAIMAAAAIAFGVAVHFRPSELKSAYYINIAICTIAATAYYAMAVNYQDLTMNGERQVVYARYIDWVLTTPLLLLDLIVMTKMGGVMISWVIGADIFMIVFGILGAFEDEHKFKWVYFIAGCVMQAVLTYGMYNATWKDDLKKSPEYHSSYVSLLVFLSILWVFYPVVWAFGSGSGVLSVDNEAILMGILDVLAKPLFGMGCLIAHETI", ) self.assertEqual(alignment.target.annotations["hmm_name"], "3AM6_A") self.assertEqual( alignment.target.annotations["hmm_description"], "rhodopsin-2; seven trans-membrane, Transport Protein; HET: RET, CLR; 3.2A {Acetabularia acetabulum}; Related PDB entries: 3AM6_B 3AM6_C 3AM6_D", ) self.assertEqual( alignment[0], "TETGMIAQWIVFAIMAAAAIAFGVAVHFRP-SELKSAYYINIAICTIAATAYYAMAVNYQDLTMN---GERQVVYARYIDWVLTTPLLLLDLIVMTKMGGVMISWVIGADIFMIVFGILGAFEDEHKFKWVYFIAGCVMQAVLTYGMYNATWKDDLKKSPEYHSSYVSLLVFLSILWVFYPVVWAFG-SGSGVLSVDNEAILMGILDVLAKPLFGMGCLIAHETI", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CHHHHHHHHHHHHHHHHHHHHHHHHGGGCCCHHHHHHHHHHHHHHHHHHHHHHHTTTSCCBSSSBBCCTHHHHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHTHHHHHHCCCCCCSSSCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cHHHHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHHHHHHHhcccccccCCcccchHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhCCccchHHHHHHHHHHHHHHHHHHHHHhhHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCCCChHHHHHHHHHHHHHhhHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 3AM6_A 5 TETGMIAQWIVFAIMAAAAIAFGVAVHFRP-SELKSAYYINIAICTIAATAYYAMAVNYQ 0 .....|......|.|......|.|......-...|..|.|......||.|.|..|...|. 4Y9H:A|PD 0 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG 3AM6_A 64 DLTMN---GERQVVYARYIDWVLTTPLLLLDLIVMTKMGGVMISWVIGADIFMIVFGILG 60 .....---.......|||.||..|||||||||..........|....|||..||..|..| 4Y9H:A|PD 60 LTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVG 3AM6_A 121 AFEDEHKFKWVYFIAGCVMQAVLTYGMYNATWKDDLKKSPEYHSSYVSLLVFLSILWVFY 120 |.........|.............|..............||..|....|......||..| 4Y9H:A|PD 120 ALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAY 3AM6_A 181 PVVWAFG-SGSGVLSVDNEAILMGILDVLAKPLFGMGCLIAHETI 225 180 ||||..|-.|.|......|..|...|||.||..||...|...... 225 4Y9H:A|PD 180 PVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIF 225 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 5, 35, 35, 69, 69, 188, 188, 225], [ 0, 30, 31, 65, 68, 187, 188, 225]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'E', 'T', 'G', 'M', 'I', 'A', 'Q', 'W', 'I', 'V', 'F', 'A', 'I', 'M', 'A', 'A', 'A', 'A', 'I', 'A', 'F', 'G', 'V', 'A', 'V', 'H', 'F', 'R', 'P', '-', 'S', 'E', 'L', 'K', 'S', 'A', 'Y', 'Y', 'I', 'N', 'I', 'A', 'I', 'C', 'T', 'I', 'A', 'A', 'T', 'A', 'Y', 'Y', 'A', 'M', 'A', 'V', 'N', 'Y', 'Q', 'D', 'L', 'T', 'M', 'N', '-', '-', '-', 'G', 'E', 'R', 'Q', 'V', 'V', 'Y', 'A', 'R', 'Y', 'I', 'D', 'W', 'V', 'L', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'I', 'V', 'M', 'T', 'K', 'M', 'G', 'G', 'V', 'M', 'I', 'S', 'W', 'V', 'I', 'G', 'A', 'D', 'I', 'F', 'M', 'I', 'V', 'F', 'G', 'I', 'L', 'G', 'A', 'F', 'E', 'D', 'E', 'H', 'K', 'F', 'K', 'W', 'V', 'Y', 'F', 'I', 'A', 'G', 'C', 'V', 'M', 'Q', 'A', 'V', 'L', 'T', 'Y', 'G', 'M', 'Y', 'N', 'A', 'T', 'W', 'K', 'D', 'D', 'L', 'K', 'K', 'S', 'P', 'E', 'Y', 'H', 'S', 'S', 'Y', 'V', 'S', 'L', 'L', 'V', 'F', 'L', 'S', 'I', 'L', 'W', 'V', 'F', 'Y', 'P', 'V', 'V', 'W', 'A', 'F', 'G', '-', 'S', 'G', 'S', 'G', 'V', 'L', 'S', 'V', 'D', 'N', 'E', 'A', 'I', 'L', 'M', 'G', 'I', 'L', 'D', 'V', 'L', 'A', 'K', 'P', 'L', 'F', 'G', 'M', 'G', 'C', 'L', 'I', 'A', 'H', 'E', 'T', 'I'], ['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 1.8e-41, places=42) self.assertAlmostEqual(alignment.annotations["Score"], 282.46) self.assertAlmostEqual(alignment.annotations["Identities"], 30) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.544) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.900) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[3:224], "EWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "EWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~lw~~~~~m~~~~~~f~~~~~~~~~~~r~~~~l~~~I~~ia~~~Y~~ma~g~g~~~~~~r~v~~~RYv~W~~TtPlll~~l~~lag~~~~~~~~~i~~~~~mi~~G~~~~~~~~~~kw~~f~~~~~~f~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~~~~~vlDi~~K~~fg~~ll~~~~~ ", ) self.assertEqual(alignment.target.id, "5JJF_A") self.assertEqual( alignment.target.seq[2:217], "LTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYVVMALGVGWVPVAERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAAT", ) self.assertEqual(alignment.target.annotations["hmm_name"], "5JJF_A") self.assertEqual( alignment.target.annotations["hmm_description"], "sensory rhodopsin; sensory rhodopsin II, transducer, membrane; HET: LFA, RET, BOG; 1.9A {Natronomonas pharaonis}; Related PDB entries: 5JJE_A 5JJN_C 2F93_A 5JJN_A 2F95_A 5JJJ_A 2KSY_A 4GYC_A 1GU8_A 1GUE_A 3QDC_A 3QAP_A 1H68_A", ) self.assertEqual( alignment[0], "LTTLFWLGAIGMLVGTLAFAWAGRDAG-SGERRYYVTLVGISGIAAVAYVVMALGVGWVPV----AERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPG-IERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAAT", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCceecCcccccHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhCCcchHHHHHHHHHHHHHHHHHHHHcHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 5JJF_A 2 LTTLFWLGAIGMLVGTLAFAWAGRDAG-SGERRYYVTLVGISGIAAVAYVVMALGVGWVP 0 ......||...|..|||.|...|....-......|........||...|..|.||.|... 4Y9H:A|PD 3 EWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTM 5JJF_A 61 V----AERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMV 60 |----........||.||..||||....|.||...|.................|..||.. 4Y9H:A|PD 63 VPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALT 5JJF_A 117 PG-IERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFI 120 ..-..|.........|.|...|.|....|..|........|....|||.||.||..||.. 4Y9H:A|PD 123 KVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVV 5JJF_A 176 WLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAAT 217 180 ||.|..|...........|...||...|||||.|.|...|. 221 4Y9H:A|PD 183 WLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 29, 29, 62, 62, 119, 119, 217], [ 3, 30, 31, 64, 68, 125, 126, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'T', 'T', 'L', 'F', 'W', 'L', 'G', 'A', 'I', 'G', 'M', 'L', 'V', 'G', 'T', 'L', 'A', 'F', 'A', 'W', 'A', 'G', 'R', 'D', 'A', 'G', '-', 'S', 'G', 'E', 'R', 'R', 'Y', 'Y', 'V', 'T', 'L', 'V', 'G', 'I', 'S', 'G', 'I', 'A', 'A', 'V', 'A', 'Y', 'V', 'V', 'M', 'A', 'L', 'G', 'V', 'G', 'W', 'V', 'P', 'V', '-', '-', '-', '-', 'A', 'E', 'R', 'T', 'V', 'F', 'A', 'P', 'R', 'Y', 'I', 'D', 'W', 'I', 'L', 'T', 'T', 'P', 'L', 'I', 'V', 'Y', 'F', 'L', 'G', 'L', 'L', 'A', 'G', 'L', 'D', 'S', 'R', 'E', 'F', 'G', 'I', 'V', 'I', 'T', 'L', 'N', 'T', 'V', 'V', 'M', 'L', 'A', 'G', 'F', 'A', 'G', 'A', 'M', 'V', 'P', 'G', '-', 'I', 'E', 'R', 'Y', 'A', 'L', 'F', 'G', 'M', 'G', 'A', 'V', 'A', 'F', 'L', 'G', 'L', 'V', 'Y', 'Y', 'L', 'V', 'G', 'P', 'M', 'T', 'E', 'S', 'A', 'S', 'Q', 'R', 'S', 'S', 'G', 'I', 'K', 'S', 'L', 'Y', 'V', 'R', 'L', 'R', 'N', 'L', 'T', 'V', 'I', 'L', 'W', 'A', 'I', 'Y', 'P', 'F', 'I', 'W', 'L', 'L', 'G', 'P', 'P', 'G', 'V', 'A', 'L', 'L', 'T', 'P', 'T', 'V', 'D', 'V', 'A', 'L', 'I', 'V', 'Y', 'L', 'D', 'L', 'V', 'T', 'K', 'V', 'G', 'F', 'G', 'F', 'I', 'A', 'L', 'D', 'A', 'A', 'A', 'T'], ['E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 5e-41, places=42) self.assertAlmostEqual(alignment.annotations["Score"], 279.16) self.assertAlmostEqual(alignment.annotations["Identities"], 27) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.447) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.000) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[6:225], "WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIF", ) self.assertEqual( alignment[1], "WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTM--VPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIF", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~lw~~~~i~~~~~l~f~~~~~~~~~~~R~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~r~v~~~RYv~W~iTtPlll~~l~~la~~~~~~~~~~~~~~~~mi~~G~~g~~~~~~~~w~~~~is~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~i~~~~e~i~~~vlDi~~K~~f~~~ll~~~~~~ ", ) self.assertEqual(alignment.target.id, "5AX0_A") self.assertEqual( alignment.target.seq[21:239], "AQWVVFAVMALAAIVFSIAVQFRPLPLRLTYYVNIAICTIAATAYYAMAVNGGDNKPTAGTGADERQVIYARYIDWVFTTPLLLLDLVLLTNMPATMIAWIMGADIAMIAFGIIGAFTVGSYKWFYFVVGCIMLAVLAWGMINPIFKEELQKHKEYTGAYTTLLIYLIVLWVIYPIVWGLGAGGHIIGVDVEIIAMGILDLLAKPLYAIGVLITVEVV", ) self.assertEqual(alignment.target.annotations["hmm_name"], "5AX0_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Rhodopsin I; PROTON TRANSPORT, MEMBRANE PROTEIN, RETINAL; HET: RET, D10, OLB, R16, D12, C14; 1.521A {Acetabularia acetabulum}; Related PDB entries: 5AX1_A 5AWZ_A", ) self.assertEqual( alignment[0], "AQWVVFAVMALAAIVFSIAVQFRP-LPLRLTYYVNIAICTIAATAYYAMAVNGGDNKPTAGTGADERQVIYARYIDWVFTTPLLLLDLVLLTNMPATMIAWIMGADIAMIAFGIIGAFTVG-SYKWFYFVVGCIMLAVLAWGMINPIFKEELQKHKEYTGAYTTLLIYLIVLWVIYPIVWGL-GAGGHIIGVDVEIIAMGILDLLAKPLYAIGVLITVEVV", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGCCCEESCGGGCEECCCHHHHHHHHHHHHHHHHHHTTBCCCHHHHHHHHHHHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHHHHHHHHHHHCGGGBSCGGGHHHHHHHHHHHHHHHHHHHHHHCCCCCTCCSCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHhcCCCcchhhHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCceeeeHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHHHHHHHHHHHHcCccccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 5AX0_A 21 AQWVVFAVMALAAIVFSIAVQFRP-LPLRLTYYVNIAICTIAATAYYAMAVNGGDNKPTA 0 ......|.|.|....|........-......|........||.|.|..|....|...--. 4Y9H:A|PD 6 WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTM--V 5AX0_A 80 GTGADERQVIYARYIDWVFTTPLLLLDLVLLTNMPATMIAWIMGADIAMIAFGIIGAFTV 60 ..|........|||.||.||||||||||.||.......|....|||..||..|..||.|. 4Y9H:A|PD 64 PFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTK 5AX0_A 140 G-SYKWFYFVVGCIMLAVLAWGMINPIFKEELQKHKEYTGAYTTLLIYLIVLWVIYPIVW 120 .-||................................|.......|.....|||..||.|| 4Y9H:A|PD 124 VYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVW 5AX0_A 199 GL-GAGGHIIGVDVEIIAMGILDLLAKPLYAIGVLITVEVV 239 180 ..-..|..|.....|......||..||.......|...... 221 4Y9H:A|PD 184 LIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIF 225 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 21, 45, 45, 77, 79, 141, 141, 201, 201, 239], [ 6, 30, 31, 63, 63, 125, 126, 186, 187, 225]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'Q', 'W', 'V', 'V', 'F', 'A', 'V', 'M', 'A', 'L', 'A', 'A', 'I', 'V', 'F', 'S', 'I', 'A', 'V', 'Q', 'F', 'R', 'P', '-', 'L', 'P', 'L', 'R', 'L', 'T', 'Y', 'Y', 'V', 'N', 'I', 'A', 'I', 'C', 'T', 'I', 'A', 'A', 'T', 'A', 'Y', 'Y', 'A', 'M', 'A', 'V', 'N', 'G', 'G', 'D', 'N', 'K', 'P', 'T', 'A', 'G', 'T', 'G', 'A', 'D', 'E', 'R', 'Q', 'V', 'I', 'Y', 'A', 'R', 'Y', 'I', 'D', 'W', 'V', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'V', 'L', 'L', 'T', 'N', 'M', 'P', 'A', 'T', 'M', 'I', 'A', 'W', 'I', 'M', 'G', 'A', 'D', 'I', 'A', 'M', 'I', 'A', 'F', 'G', 'I', 'I', 'G', 'A', 'F', 'T', 'V', 'G', '-', 'S', 'Y', 'K', 'W', 'F', 'Y', 'F', 'V', 'V', 'G', 'C', 'I', 'M', 'L', 'A', 'V', 'L', 'A', 'W', 'G', 'M', 'I', 'N', 'P', 'I', 'F', 'K', 'E', 'E', 'L', 'Q', 'K', 'H', 'K', 'E', 'Y', 'T', 'G', 'A', 'Y', 'T', 'T', 'L', 'L', 'I', 'Y', 'L', 'I', 'V', 'L', 'W', 'V', 'I', 'Y', 'P', 'I', 'V', 'W', 'G', 'L', '-', 'G', 'A', 'G', 'G', 'H', 'I', 'I', 'G', 'V', 'D', 'V', 'E', 'I', 'I', 'A', 'M', 'G', 'I', 'L', 'D', 'L', 'L', 'A', 'K', 'P', 'L', 'Y', 'A', 'I', 'G', 'V', 'L', 'I', 'T', 'V', 'E', 'V', 'V'], ['W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', '-', '-', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 1.2e-40, places=41) self.assertAlmostEqual(alignment.annotations["Score"], 279.52) self.assertAlmostEqual(alignment.annotations["Identities"], 28) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.470) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.900) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhhC", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[1:226], "RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment[1], "RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDA----DQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~w~~~~~~~~~~~~f~~~~~~~~~~r~~~~~~~~~i~~ia~~~Y~~ma~g~g~~~~~g~~v~~~RYv~W~vTtPlll~~l~~la~~~~~~~~~~~~~~i~~~~~mi~~G~~a~~~~~~~~kw~~~~~s~~~f~~il~~l~~~~~~~a~~~~~~~~~~~~~L~~~~~v~W~~YPivw~l~~~g~~~is~~~~~i~~~vlDi~~K~~f~~~ll~~~~~~~ ", ) self.assertEqual(alignment.target.id, "1XIO_A") self.assertEqual( alignment.target.seq[1:225], "NLESLLHWIYVAGMTIGALHFWSLSRNPRGVPQYEYLVAMFIPIWSGLAYMAMAIDQGKVEAAGQIAHYARYIDWMVTTPLLLLSLSWTAMQFIKKDWTLIGFLMSTQIVVITSGLIADLSERDWVRYLWYICGVCAFLIILWGIWNPLRAKTRTQSSELANLYDKLVTYFTVLWIGYPIVWIIGPSGFGWINQTIDTFLFCLLPFFSKVGFSFLDLHGLRNLN", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1XIO_A") self.assertEqual( alignment.target.annotations["hmm_description"], "ANABAENA SENSORY RHODOPSIN; signaling protein, photoreceptor; HET: PEE, RET; 2.0A {Nostoc sp. PCC 7120} SCOP: f.13.1.1; Related PDB entries: 2M3G_C 5UK6_B 5UK6_A 5UK6_C 2M3G_B 2M3G_A 4TL3_B 4TL3_A", ) self.assertEqual( alignment[0], "NLESLLHWIYVAGMTIGALHFWSLSRN-PRGVPQYEYLVAMFIPIWSGLAYMAMAIDQGKVEA----AGQIAHYARYIDWMVTTPLLLLSLSWTAMQFIKKDWTLIGFLMSTQIVVITSGLIADLSERDWVRYLWYICGVCAFLIILWGIWNPLRAKTRTQSSELANLYDKLVTYFTVLWIGYPIVWIIGPSGFGWINQTIDTFLFCLLPFFSKVGFSFLDLHGLRNLN", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CHHHHHHHHHHHHHHHHHHHHHHHHTSCTTCCHHHHHHHHHHHHHHHHHHHHHHHCCTTHHHHHHHHHHHHHHHHHHHHHHTTTSCCCHHHHHHHHHHHHHHHHHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCSSCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHTT ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " chHHHHHHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHHHHHHHHHHHhccCceecccccccHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc ", ) self.assertEqual( str(alignment), """\ 1XIO_A 1 NLESLLHWIYVAGMTIGALHFWSLSRN-PRGVPQYEYLVAMFIPIWSGLAYMAMAIDQGK 0 ..|........|.|..|.|.|......-........|......|......|..|....|. 4Y9H:A|PD 1 RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGL 1XIO_A 60 VEA----AGQIAHYARYIDWMVTTPLLLLSLSWTAMQFIKKDWTLIGFLMSTQIVVITSG 60 ...----.......|||.||..|||||||.|......----|...|..|.......|..| 4Y9H:A|PD 61 TMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDA----DQGTILALVGADGIMIGTG 1XIO_A 116 LIADLSERDWVRYLWYICGVCAFLIILWGIWNPLRAKTRTQSSELANLYDKLVTYFTVLW 120 |...|......|..|......|.|.||.........|......|.|.....|.....||| 4Y9H:A|PD 117 LVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLW 1XIO_A 176 IGYPIVWIIGPSGFGWINQTIDTFLFCLLPFFSKVGFSFLDLHGLRNLN 225 180 ..||.||.||..|.|.....|.|.||..|....||||....|....... 229 4Y9H:A|PD 177 SAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 226 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 28, 28, 63, 63, 93, 97, 225], [ 1, 28, 29, 64, 68, 98, 98, 226]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['N', 'L', 'E', 'S', 'L', 'L', 'H', 'W', 'I', 'Y', 'V', 'A', 'G', 'M', 'T', 'I', 'G', 'A', 'L', 'H', 'F', 'W', 'S', 'L', 'S', 'R', 'N', '-', 'P', 'R', 'G', 'V', 'P', 'Q', 'Y', 'E', 'Y', 'L', 'V', 'A', 'M', 'F', 'I', 'P', 'I', 'W', 'S', 'G', 'L', 'A', 'Y', 'M', 'A', 'M', 'A', 'I', 'D', 'Q', 'G', 'K', 'V', 'E', 'A', '-', '-', '-', '-', 'A', 'G', 'Q', 'I', 'A', 'H', 'Y', 'A', 'R', 'Y', 'I', 'D', 'W', 'M', 'V', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'S', 'L', 'S', 'W', 'T', 'A', 'M', 'Q', 'F', 'I', 'K', 'K', 'D', 'W', 'T', 'L', 'I', 'G', 'F', 'L', 'M', 'S', 'T', 'Q', 'I', 'V', 'V', 'I', 'T', 'S', 'G', 'L', 'I', 'A', 'D', 'L', 'S', 'E', 'R', 'D', 'W', 'V', 'R', 'Y', 'L', 'W', 'Y', 'I', 'C', 'G', 'V', 'C', 'A', 'F', 'L', 'I', 'I', 'L', 'W', 'G', 'I', 'W', 'N', 'P', 'L', 'R', 'A', 'K', 'T', 'R', 'T', 'Q', 'S', 'S', 'E', 'L', 'A', 'N', 'L', 'Y', 'D', 'K', 'L', 'V', 'T', 'Y', 'F', 'T', 'V', 'L', 'W', 'I', 'G', 'Y', 'P', 'I', 'V', 'W', 'I', 'I', 'G', 'P', 'S', 'G', 'F', 'G', 'W', 'I', 'N', 'Q', 'T', 'I', 'D', 'T', 'F', 'L', 'F', 'C', 'L', 'L', 'P', 'F', 'F', 'S', 'K', 'V', 'G', 'F', 'S', 'F', 'L', 'D', 'L', 'H', 'G', 'L', 'R', 'N', 'L', 'N'], ['R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', '-', '-', '-', '-', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 1.4e-40, places=41) self.assertAlmostEqual(alignment.annotations["Score"], 282.56) self.assertAlmostEqual(alignment.annotations["Identities"], 32) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.598) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.300) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[6:224], "WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVP----------------FGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVY-SYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~lw~~~~i~~l~~~vf~~~s~~~~~~~~R~~~~l~~~i~~va~~aY~~Ma~g~G~~~v~~~~~~~~~~~~~~~g~~~~~~r~v~~~RYv~W~iTtPlll~~l~llag~~~~~i~~~v~~~~~mi~~Gl~gal~~~~~~~kw~~f~~g~~~~~~i~~~l~~~~~~~a~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~G~~vi~~~~e~i~y~ilDi~~K~~f~~~ll~~~~~ ", ) self.assertEqual(alignment.target.id, "5B0W_G") self.assertEqual( alignment.target.seq[36:269], "SLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAGTADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTS", ) self.assertEqual(alignment.target.annotations["hmm_name"], "5B0W_G") self.assertEqual( alignment.target.annotations["hmm_description"], "Halorhodopsin; seven trans-membrane helices, retinylidene protein; HET: RET, L3P, BNG, 22B; 1.7A {Natronomonas pharaonis DSM 2160}; Related PDB entries: 5B0W_D 3QBI_D 5ETZ_A 3ABW_D 3A7K_B 5ETZ_D 3QBK_D 3ABW_A 3VVK_C 4QRY_G 5B0W_F 3QBL_A 3ABW_B 3QBG_B 4QRY_E 3QBK_A 3QBI_B 3QBG_D 3VVK_B 3QBG_A 4QRY_C 5B0W_B 4QRY_F 3QBL_D 5B0W_A 3VVK_D 4QRY_A 5B0W_E 3VVK_A 3QBL_B 5ETZ_B 3A7K_A 3QBI_A 4QRY_B 3QBK_B 3VVK_F 3A7K_D 3VVK_E", ) self.assertEqual( alignment[0], "SLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAG--TADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTS", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCEEECCCTTCTTTTCBCCBTTBCCBSEEECTHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHBTTTTCSBCHHHHHHHHHHHHCCCCCCHHHHHHHHHTT ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCceEEecccccccCCceeeecCCccCceeccHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHh ", ) self.assertEqual( str(alignment), """\ 5B0W_G 36 SLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEM 0 .|....||.||..|.|.....|..||.||.....|.|||......|.....|.......- 4Y9H:A|PD 6 WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVP- 5B0W_G 96 PAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFD 60 ---------------.........|.||..|...||..||.|.||..............| 4Y9H:A|PD 65 ---------------FGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGAD 5B0W_G 156 IAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAG--TADIFSTL 120 ..|..|||..|||...-..|..|.|||.|.....||.|.......|....--.|..|..| 4Y9H:A|PD 110 GIMIGTGLVGALTKVY-SYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVL 5B0W_G 214 KLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTS 269 180 ...|||.|..||.||..|.||....|..........||..||..|...||..... 235 4Y9H:A|PD 169 RNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 36, 95, 111, 172, 173, 206, 206, 269], [ 6, 65, 65, 126, 126, 159, 161, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['S', 'L', 'Y', 'I', 'N', 'I', 'A', 'L', 'A', 'G', 'L', 'S', 'I', 'L', 'L', 'F', 'V', 'F', 'M', 'T', 'R', 'G', 'L', 'D', 'D', 'P', 'R', 'A', 'K', 'L', 'I', 'A', 'V', 'S', 'T', 'I', 'L', 'V', 'P', 'V', 'V', 'S', 'I', 'A', 'S', 'Y', 'T', 'G', 'L', 'A', 'S', 'G', 'L', 'T', 'I', 'S', 'V', 'L', 'E', 'M', 'P', 'A', 'G', 'H', 'F', 'A', 'E', 'G', 'S', 'S', 'V', 'M', 'L', 'G', 'G', 'E', 'E', 'V', 'D', 'G', 'V', 'V', 'T', 'M', 'W', 'G', 'R', 'Y', 'L', 'T', 'W', 'A', 'L', 'S', 'T', 'P', 'M', 'I', 'L', 'L', 'A', 'L', 'G', 'L', 'L', 'A', 'G', 'S', 'N', 'A', 'T', 'K', 'L', 'F', 'T', 'A', 'I', 'T', 'F', 'D', 'I', 'A', 'M', 'C', 'V', 'T', 'G', 'L', 'A', 'A', 'A', 'L', 'T', 'T', 'S', 'S', 'H', 'L', 'M', 'R', 'W', 'F', 'W', 'Y', 'A', 'I', 'S', 'C', 'A', 'C', 'F', 'I', 'V', 'V', 'L', 'Y', 'I', 'L', 'L', 'V', 'E', 'W', 'A', 'Q', 'D', 'A', 'K', 'A', 'A', 'G', '-', '-', 'T', 'A', 'D', 'I', 'F', 'S', 'T', 'L', 'K', 'L', 'L', 'T', 'V', 'V', 'M', 'W', 'L', 'G', 'Y', 'P', 'I', 'V', 'W', 'A', 'L', 'G', 'V', 'E', 'G', 'V', 'A', 'V', 'L', 'P', 'V', 'G', 'Y', 'T', 'S', 'W', 'A', 'Y', 'S', 'A', 'L', 'D', 'I', 'V', 'A', 'K', 'Y', 'I', 'F', 'A', 'F', 'L', 'L', 'L', 'N', 'Y', 'L', 'T', 'S'], ['W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', '-', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 2.2e-40, places=41) self.assertAlmostEqual(alignment.annotations["Score"], 279.46) self.assertAlmostEqual(alignment.annotations["Identities"], 34) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.606) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhhC", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[6:226], "WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment[1], "WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPF------GGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYS--YRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIV-PLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~lw~~~~~~~~~~l~f~~~~~~~~~~~~R~~~~l~~~i~~iaa~~Y~~ma~g~g~~~v~~~~~~~~~~~~~~~~~~RYvdW~vTtPlll~~l~~lag~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~kw~~~~is~~~~~~i~~~l~~~~~~~a~~~~~~~~~~~l~~~~~v~W~~YPivw~l~~~G~~~i~s~~~e~i~y~ilDv~~K~~fg~~ll~~~~~~~ ", ) self.assertEqual(alignment.target.id, "2JAF_A") self.assertEqual( alignment.target.seq[31:257], "SLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLLSGLTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLADVDLGSLFTVIAADIGMCVTGLAAAMTTSALLFRWAFYAISCAFFVVVLSALVTDWAASASSAGTAEIFDTLRVLVVVLWLGYPIVWAVGVEGLALVQSVGATSWAYSVLDVFAKYVFAFILLRWVANNE", ) self.assertEqual(alignment.target.annotations["hmm_name"], "2JAF_A") self.assertEqual( alignment.target.annotations["hmm_description"], "HALORHODOPSIN; CHROMOPHORE, CHLORIDE PUMP, ION TRANSPORT; HET: BOG, RET, PLM; 1.7A {HALOBACTERIUM SALINARIUM} SCOP: f.13.1.1; Related PDB entries: 2JAG_A 5AHZ_A 5G36_A 5AHY_A 1E12_A", ) self.assertEqual( alignment[0], "SLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLLSGLTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLADVDLGSLFTVIAADIGMCVTGLAAAMTTS-ALLFRWAFYAISCAFFVVVLSALVTDWAASAS--SAGTAEIFDTLRVLVVVLWLGYPIVWAVGVEGLALVQSVGATSWAYSVLDVFAKYVFAFILLRWVANNE", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHHHTTTCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCEEEECCTTSTTTTSEEEECHHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCSSCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHTH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHcCCCCCCccHHHHHHHHHHHHHHHHHHHHHcCCCceeeecccCCcccCCeEeeeHHHHHHHHhHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHHHHHHHHHhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHccccccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhch ", ) self.assertEqual( str(alignment), """\ 2JAF_A 31 SLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLLSGLTVGMIEM 0 .|....||.|...|.|...|..............|...|......||..|.|....|... 4Y9H:A|PD 6 WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPF 2JAF_A 91 PAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLADVDLGSLFTVIAADIGMCVTGLAA 60 ------.||.....|.||..|...||..||.|.||.|.|.|.......||..|..|||.. 4Y9H:A|PD 66 ------GGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVG 2JAF_A 151 AMTTS-ALLFRWAFYAISCAFFVVVLSALVTDWAASAS--SAGTAEIFDTLRVLVVVLWL 120 |.|..-.--.|....|||.|.....|..|.......|.--....|..|..||...||||. 4Y9H:A|PD 120 ALTKVYS--YRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWS 2JAF_A 208 GYPIVWAVGVEGLALVQSVGATSWAYSVLDVFAKYVFAFILLRWVANNE 257 180 .||.||..|.||...|-..........||||.||..|..||||..|... 229 4Y9H:A|PD 178 AYPVVWLIGSEGAGIV-PLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 226 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 31, 91, 97, 156, 156, 157, 159, 188, 188, 224, 225, 257], [ 6, 66, 66, 125, 126, 127, 127, 156, 158, 194, 194, 226]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['S', 'L', 'W', 'V', 'N', 'V', 'A', 'L', 'A', 'G', 'I', 'A', 'I', 'L', 'V', 'F', 'V', 'Y', 'M', 'G', 'R', 'T', 'I', 'R', 'P', 'G', 'R', 'P', 'R', 'L', 'I', 'W', 'G', 'A', 'T', 'L', 'M', 'I', 'P', 'L', 'V', 'S', 'I', 'S', 'S', 'Y', 'L', 'G', 'L', 'L', 'S', 'G', 'L', 'T', 'V', 'G', 'M', 'I', 'E', 'M', 'P', 'A', 'G', 'H', 'A', 'L', 'A', 'G', 'E', 'M', 'V', 'R', 'S', 'Q', 'W', 'G', 'R', 'Y', 'L', 'T', 'W', 'A', 'L', 'S', 'T', 'P', 'M', 'I', 'L', 'L', 'A', 'L', 'G', 'L', 'L', 'A', 'D', 'V', 'D', 'L', 'G', 'S', 'L', 'F', 'T', 'V', 'I', 'A', 'A', 'D', 'I', 'G', 'M', 'C', 'V', 'T', 'G', 'L', 'A', 'A', 'A', 'M', 'T', 'T', 'S', '-', 'A', 'L', 'L', 'F', 'R', 'W', 'A', 'F', 'Y', 'A', 'I', 'S', 'C', 'A', 'F', 'F', 'V', 'V', 'V', 'L', 'S', 'A', 'L', 'V', 'T', 'D', 'W', 'A', 'A', 'S', 'A', 'S', '-', '-', 'S', 'A', 'G', 'T', 'A', 'E', 'I', 'F', 'D', 'T', 'L', 'R', 'V', 'L', 'V', 'V', 'V', 'L', 'W', 'L', 'G', 'Y', 'P', 'I', 'V', 'W', 'A', 'V', 'G', 'V', 'E', 'G', 'L', 'A', 'L', 'V', 'Q', 'S', 'V', 'G', 'A', 'T', 'S', 'W', 'A', 'Y', 'S', 'V', 'L', 'D', 'V', 'F', 'A', 'K', 'Y', 'V', 'F', 'A', 'F', 'I', 'L', 'L', 'R', 'W', 'V', 'A', 'N', 'N', 'E'], ['W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', '-', '-', '-', '-', '-', '-', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', '-', '-', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', '-', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 2.6e-40, places=41) self.assertAlmostEqual(alignment.annotations["Score"], 266.44) self.assertAlmostEqual(alignment.annotations["Identities"], 99) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.599) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.100) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:217], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLI", ) self.assertEqual( alignment[1], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~va~~~Y~~ma~~~g~~~~~~~~~~~~~~~~RYv~W~iTtPlll~~l~~l~g~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~~~~~~~~~Di~~K~~fg~~", ) self.assertEqual(alignment.target.id, "1C8S_A") self.assertEqual( alignment.target.seq[1:196], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLNLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLI", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1C8S_A") self.assertEqual( alignment.target.annotations["hmm_description"], "BACTERIORHODOPSIN MUTANT/LIPID COMPLEX; ION PUMP, MEMBRANE PROTEIN, RETINAL; HET: LI1, SQU, RET; 2.0A {Halobacterium salinarum} SCOP: f.13.1.1", ) self.assertEqual( alignment[0], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLNLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLF----------------------NVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLI", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCTTHHHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCBCCEETTEECCBCHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSTTTTCCSCHHHHHHHHHHHHHCCCCCHHHC", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCcHHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCCCceeccCCCCCCcchhHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHhHHhHhcC", ) self.assertEqual( str(alignment), """\ 1C8S_A 1 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 4Y9H:A|PD 0 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG 1C8S_A 61 LTMVPFGGEQNPIYWARYADWLFTTPLLLLNLALLVDADQGTILALVGADGIMIGTGLVG 60 ||||||||||||||||||||||||||||||.||||||||||||||||||||||||||||| 4Y9H:A|PD 60 LTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVG 1C8S_A 121 ALTKVYSYRFVWWAISTAAMLYILYVLF----------------------NVTVVLWSAY 120 ||||||||||||||||||||||||||||----------------------|||||||||| 4Y9H:A|PD 120 ALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAY 1C8S_A 159 PVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLI 196 180 ||||||||||||||||||||||||||||||||||||| 217 4Y9H:A|PD 180 PVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLI 217 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 149, 149, 196], [ 0, 148, 170, 217]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'N', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I'], ['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 4.7e-39, places=40) self.assertAlmostEqual(alignment.annotations["Score"], 273.19) self.assertAlmostEqual(alignment.annotations["Identities"], 22) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.327) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:224], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFG-------GEQNPI--YWARYADWLFTTPLLLLDLALLVDADQGTIL----ALVGADGIMIGTGLVGALTKV--YSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSE----GAGIV--PLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~s~~lw~~~~~~~~~~l~f~~~~~~~~~~~R~~~~l~~~i~~vaa~~Y~~ma~~~g~~~~~~~~~~~~~~~~~~~~~~~~~RYvdW~vTtPlll~~l~llag~~~~~~~~~~~~~v~~~~~Mi~~G~~g~~~~~~~~~~kw~~f~ig~~~~~~vl~~l~~~~~~~a~~~~~~~~~~~~~L~~~~~v~W~~YPivw~l~~~~~~~G~~li~~~~~~~~i~y~ilDv~aK~~fg~~ll~~~~~ ", ) self.assertEqual(alignment.target.id, "4XTL_A") self.assertEqual( alignment.target.seq[24:268], "YQFTSHILTLGYAVMLAGLLYFILTIKNVDKKFQMSNILSAVVMVSAFLLLYAQAQNWTSSFTFNEEVGRYFLDPSGDLFNNGYRYLNWLIDVPMLLFQILFVVSLTTSKFSSVRNQFWFSGAMMIITGYIGQFYEVSNLTAFLVWGAISSAFFFHILWVMKKVINEGKEGISPAGQKILSNIWILFLISWTLYPGAYLMPYLTGVDGFLYSEDGVMARQLVYTIADVSSXVIYGVLLGNLAIT", ) self.assertEqual(alignment.target.annotations["hmm_name"], "4XTL_A") self.assertEqual( alignment.target.annotations["hmm_description"], "KR2; ion pump, membrane protein; HET: GOL, LFA, LYR; 1.45A {Dokdonia eikasta}; Related PDB entries: 3X3B_A 3X3C_A 5JRF_A 4XTO_D 4XTN_C 4XTN_H 4XTN_A 4XTO_E 4XTN_B 4XTN_D 4XTO_A 4XTN_G 4XTO_B 4XTN_F 4XTO_C 4XTN_I 4XTN_J 4XTN_E", ) self.assertEqual( alignment[0], "YQFTSHILTLGYAVMLAGLLYFILTIKNVD-KKFQMSNILSAVVMVSAFLLLYAQAQNWTSSFTFNEEVGRYFLDPSGDLFNNGYRYLNWLIDVPMLLFQILFVVSLTTSKFSSVRNQFWFSGAMMIITGYIGQFYEVSNLTAFLVWGAISSAFFFHILWVMKKVINEGKEGISPAGQKILSNIWILFLISWTLYPGAYLMPYLTGVDGFLYSEDGVMARQLVYTIADVSSXVIYGVLLGNLAIT", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHHHHHHHHTGGGSCGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEETTTTEEEECTTSCCCCTHHHHHHHHHHHHHHHHHGGGTSCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTCTTSTTSSHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " hHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHHHHHHHHHHHHHHHHHHHhchhhcccccchhcccccCCCCCccchHHHHHHHHHHHHHHHHHHHHHHcccccchHHHHHHHHHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 4XTL_A 24 YQFTSHILTLGYAVMLAGLLYFILTIKNVD-KKFQMSNILSAVVMVSAFLLLYAQAQNWT 0 .......|.||.|.|..|.|||......|.-............|...||........... 4Y9H:A|PD 0 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG 4XTL_A 83 SSFTFNEEVGRYFLDPSGDLFNNGYRYLNWLIDVPMLLFQILFVVSLTTSKFSSVRNQFW 60 .......-------......--...||..||...|.||......|........----... 4Y9H:A|PD 60 LTMVPFG-------GEQNPI--YWARYADWLFTTPLLLLDLALLVDADQGTIL----ALV 4XTL_A 143 FSGAMMIITGYIGQFYEVSNLTAFLVWGAISSAFFFHILWVMKKVINEGKEGISPAGQKI 120 .....||.||..|....|--.....||.|||.|....||.|.........|...|..... 4Y9H:A|PD 107 GADGIMIGTGLVGALTKV--YSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVAST 4XTL_A 203 LSNIWILFLISWTLYPGAYLMPYLTGVDGFLYSEDGVMARQLVYTIADVSSXVIYGVLLG 180 ...........|..||...|....----|....--......|.....|||..|..|..|. 4Y9H:A|PD 165 FKVLRNVTVVLWSAYPVVWLIGSE----GAGIV--PLNIETLLFMVLDVSAKVGFGLILL 4XTL_A 263 NLAIT 268 240 ..... 245 4Y9H:A|PD 219 RSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 24, 54, 54, 90, 97, 103, 105, 136, 140, 161, 163, 227, 231, 236, 238, 268], [ 0, 30, 31, 67, 67, 73, 73, 104, 104, 125, 125, 189, 189, 194, 194, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['Y', 'Q', 'F', 'T', 'S', 'H', 'I', 'L', 'T', 'L', 'G', 'Y', 'A', 'V', 'M', 'L', 'A', 'G', 'L', 'L', 'Y', 'F', 'I', 'L', 'T', 'I', 'K', 'N', 'V', 'D', '-', 'K', 'K', 'F', 'Q', 'M', 'S', 'N', 'I', 'L', 'S', 'A', 'V', 'V', 'M', 'V', 'S', 'A', 'F', 'L', 'L', 'L', 'Y', 'A', 'Q', 'A', 'Q', 'N', 'W', 'T', 'S', 'S', 'F', 'T', 'F', 'N', 'E', 'E', 'V', 'G', 'R', 'Y', 'F', 'L', 'D', 'P', 'S', 'G', 'D', 'L', 'F', 'N', 'N', 'G', 'Y', 'R', 'Y', 'L', 'N', 'W', 'L', 'I', 'D', 'V', 'P', 'M', 'L', 'L', 'F', 'Q', 'I', 'L', 'F', 'V', 'V', 'S', 'L', 'T', 'T', 'S', 'K', 'F', 'S', 'S', 'V', 'R', 'N', 'Q', 'F', 'W', 'F', 'S', 'G', 'A', 'M', 'M', 'I', 'I', 'T', 'G', 'Y', 'I', 'G', 'Q', 'F', 'Y', 'E', 'V', 'S', 'N', 'L', 'T', 'A', 'F', 'L', 'V', 'W', 'G', 'A', 'I', 'S', 'S', 'A', 'F', 'F', 'F', 'H', 'I', 'L', 'W', 'V', 'M', 'K', 'K', 'V', 'I', 'N', 'E', 'G', 'K', 'E', 'G', 'I', 'S', 'P', 'A', 'G', 'Q', 'K', 'I', 'L', 'S', 'N', 'I', 'W', 'I', 'L', 'F', 'L', 'I', 'S', 'W', 'T', 'L', 'Y', 'P', 'G', 'A', 'Y', 'L', 'M', 'P', 'Y', 'L', 'T', 'G', 'V', 'D', 'G', 'F', 'L', 'Y', 'S', 'E', 'D', 'G', 'V', 'M', 'A', 'R', 'Q', 'L', 'V', 'Y', 'T', 'I', 'A', 'D', 'V', 'S', 'S', 'X', 'V', 'I', 'Y', 'G', 'V', 'L', 'L', 'G', 'N', 'L', 'A', 'I', 'T'], ['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', '-', '-', '-', '-', '-', '-', '-', 'G', 'E', 'Q', 'N', 'P', 'I', '-', '-', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', 'I', 'L', '-', '-', '-', '-', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', '-', '-', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', '-', '-', '-', '-', 'G', 'A', 'G', 'I', 'V', '-', '-', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 1.3e-38, places=39) self.assertAlmostEqual(alignment.annotations["Score"], 275.60) self.assertAlmostEqual(alignment.annotations["Identities"], 16) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.231) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 6.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhhC", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:226], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment[1], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAIT---TLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQ---GTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESM-RPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~lwv~f~~m~~~~l~f~~~~~r~~~~~r~~~~l~~~~~~I~~ia~~sY~~ma~~~~~~gr~v~~~RYvdWliTtPLLL~~L~lLag~~~~~~~~~~~lv~~d~lMI~~G~~gal~~~~~kw~~f~is~~~~l~l~~~l~~~~~~a~~~~~~~~~~~~~~~L~~l~~v~W~lYPIvw~L~~eG~~~is~~~e~i~y~ilDilsKv~fg~ll~~~~~~i~ ", ) self.assertEqual(alignment.target.id, "5ZIH_B") self.assertEqual( alignment.target.seq[87:311], "KIGAQVCQWIAFSIAIALLTFYGFSAWKATCGWEEVYVCCVEVLFVTLEIFKEFSSPATVYLSTGNHAYCLRYFEWLLSCPVILIKLSNLSGLKNDYSKRTMGLIVSCVGMIVFGMAAGLATDWLKWLLYIVSCIYGGYMYFQAAKCYVEANHSVPKGHCRMVVKLMAYAYFASWGSYPILWAVGPEGLLKLSPYANSIGHSICDIIAXEFWTFLAHHLRIKIH", ) self.assertEqual(alignment.target.annotations["hmm_name"], "5ZIH_B") self.assertEqual( alignment.target.annotations["hmm_description"], "Sensory opsin A,Chrimson; membrane protein, rhodopsin, ion channel; HET: OLC, LYR; 2.6A {Chlamydomonas reinhardtii}; Related PDB entries: 5ZIH_A", ) self.assertEqual( alignment[0], "KIGAQVCQWIAFSIAIALLTFYGFSAWKAT-CGWEEVYVCCVEVLFVTLEIFKEFSSPATVYLS-------TGNHAYCLRYFEWLLSCPVILIKLSNLSGLKNDYSKRTMGLIVSCVGMIVFGMAAGLATD-WLKWLLYIVSCIYGGYMYFQAAKCYVEANHSVPKGHCRMVVKLMAYAYFASWGSYPILWAVGPEGLLKLSPYANSIGHSICDIIAXEFWTFLAHHLRIKIH", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHHHHHHCCCCCTTHHHHHHHHHHHHHHHHHHHHTTSTTTSEEBTTSCEECHHHHHHHHHHHHHHHHHHHTCSSSSSCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHTHHHHHHHHSTTTTSCSCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " chhHHHHHHHHHHHHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHcCcCCCccccHHHHHHHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHCcccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 5ZIH_B 87 KIGAQVCQWIAFSIAIALLTFYGFSAWKAT-CGWEEVYVCCVEVLFVTLEIFKEFSSPAT 0 ..............................-......|...---..|....|....|... 4Y9H:A|PD 0 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAIT---TLVPAIAFTMYLSMLL 5ZIH_B 146 VYLS-------TGNHAYCLRYFEWLLSCPVILIKLSNLSGLKNDYSKRTMGLIVSCVGMI 60 .|..-------..|..|..||..||...|..|..|..|.....---.....|......|| 4Y9H:A|PD 57 GYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQ---GTILALVGADGIMI 5ZIH_B 199 VFGMAAGLATD-WLKWLLYIVSCIYGGYMYFQAAKCYVEANHSVPKGHCRMVVKLMAYAY 120 ..|....|...-.........|.....|..............|.-........|...... 4Y9H:A|PD 114 GTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESM-RPEVASTFKVLRNVT 5ZIH_B 258 FASWGSYPILWAVGPEGLLKLSPYANSIGHSICDIIAXEFWTFLAHHLRIKIH 311 180 ...|..||..|..|.||................|..|...........|.... 233 4Y9H:A|PD 173 VVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 226 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 87, 117, 117, 127, 130, 150, 150, 182, 185, 210, 210, 242, 243, 311], [ 0, 30, 31, 41, 41, 61, 68, 100, 100, 125, 126, 158, 158, 226]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'I', 'G', 'A', 'Q', 'V', 'C', 'Q', 'W', 'I', 'A', 'F', 'S', 'I', 'A', 'I', 'A', 'L', 'L', 'T', 'F', 'Y', 'G', 'F', 'S', 'A', 'W', 'K', 'A', 'T', '-', 'C', 'G', 'W', 'E', 'E', 'V', 'Y', 'V', 'C', 'C', 'V', 'E', 'V', 'L', 'F', 'V', 'T', 'L', 'E', 'I', 'F', 'K', 'E', 'F', 'S', 'S', 'P', 'A', 'T', 'V', 'Y', 'L', 'S', '-', '-', '-', '-', '-', '-', '-', 'T', 'G', 'N', 'H', 'A', 'Y', 'C', 'L', 'R', 'Y', 'F', 'E', 'W', 'L', 'L', 'S', 'C', 'P', 'V', 'I', 'L', 'I', 'K', 'L', 'S', 'N', 'L', 'S', 'G', 'L', 'K', 'N', 'D', 'Y', 'S', 'K', 'R', 'T', 'M', 'G', 'L', 'I', 'V', 'S', 'C', 'V', 'G', 'M', 'I', 'V', 'F', 'G', 'M', 'A', 'A', 'G', 'L', 'A', 'T', 'D', '-', 'W', 'L', 'K', 'W', 'L', 'L', 'Y', 'I', 'V', 'S', 'C', 'I', 'Y', 'G', 'G', 'Y', 'M', 'Y', 'F', 'Q', 'A', 'A', 'K', 'C', 'Y', 'V', 'E', 'A', 'N', 'H', 'S', 'V', 'P', 'K', 'G', 'H', 'C', 'R', 'M', 'V', 'V', 'K', 'L', 'M', 'A', 'Y', 'A', 'Y', 'F', 'A', 'S', 'W', 'G', 'S', 'Y', 'P', 'I', 'L', 'W', 'A', 'V', 'G', 'P', 'E', 'G', 'L', 'L', 'K', 'L', 'S', 'P', 'Y', 'A', 'N', 'S', 'I', 'G', 'H', 'S', 'I', 'C', 'D', 'I', 'I', 'A', 'X', 'E', 'F', 'W', 'T', 'F', 'L', 'A', 'H', 'H', 'L', 'R', 'I', 'K', 'I', 'H'], ['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', '-', '-', '-', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', '-', '-', '-', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', '-', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 3.1e-38, places=39) self.assertAlmostEqual(alignment.annotations["Score"], 261.06) self.assertAlmostEqual(alignment.annotations["Identities"], 26) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.424) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.300) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[5:224], "IWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "IWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDA----DQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAES--MRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~lw~~~~~~~~~~~~~~~~~~~~~~~~R~~~~l~~~i~~ia~~~Y~~m~~~~~~~g~~~~~~RYv~W~~TtPlll~~l~~l~~~~~~~~~~~~~~~~~~~~~mi~~G~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~i~~~~e~i~~~ilDv~~K~~f~~~ll~~~~~ ", ) self.assertEqual(alignment.target.id, "4JQ6_C") self.assertEqual( alignment.target.seq[12:226], "ISFWLAAAIMLASTVFFFVERSDVPVKWKTSLTVAGLVTGVAFWHYLYMRGVWIYAGETPTVFRYIDWLITVPLQIIEFYLIIAAVTAISSAVFWKLLIASLVMLIGGFIGEAGLGDVVVWWIVGMIAWLYIIYEIFLGETAKANAGSGNAASQQAFNTIKWIVTVGWAIYPIGYAWGYFGDGLNEDALNIVYNLADLINKAAFGLAIWAAAMK", ) self.assertEqual(alignment.target.annotations["hmm_name"], "4JQ6_C") self.assertEqual( alignment.target.annotations["hmm_description"], "Proteorhodopsin; retinylidene protein, ion transport, PROTON; HET: LI1, RET; 2.31A {uncultured bacterium} SCOP: f.13.1.0; Related PDB entries: 4JQ6_A 4JQ6_B", ) self.assertEqual( alignment[0], "ISFWLAAAIMLASTVFFFVERSDVP-VKWKTSLTVAGLVTGVAFWHYLYMRGVWIY-------AGETPTVFRYIDWLITVPLQIIEFYLIIAAVTAISSAVFWKLLIASLVMLIGGFIGEAGLGD--VVVWWIVGMIAWLYIIYEIFLGETAKANAGSGNAASQQAFNTIKWIVTVGWAIYPIGYAW-GYFGDGLNEDALNIVYNLADLINKAAFGLAIWAAAMK", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHHTTCCTHHHHHHHHCCCCCHHHHHHHHHHHHSSSSCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHHHHHHHcchhhcCCCCchHHHHHHHhHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHhhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 4JQ6_C 12 ISFWLAAAIMLASTVFFFVERSDVP-VKWKTSLTVAGLVTGVAFWHYLYMRGVWIY---- 0 |...|..|.|...|..|.|....|.-...|.......||...||..||.|......---- 4Y9H:A|PD 5 IWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVP 4JQ6_C 67 ---AGETPTVFRYIDWLITVPLQIIEFYLIIAAVTAISSAVFWKLLIASLVMLIGGFIGE 60 ---........||.|||.|.||......|...|----.......|..|...|...|..|. 4Y9H:A|PD 65 FGGEQNPIYWARYADWLFTTPLLLLDLALLVDA----DQGTILALVGADGIMIGTGLVGA 4JQ6_C 124 AGLGD--VVVWWIVGMIAWLYIIYEIFLGETAKANAGSGNAASQQAFNTIKWIVTVGWAI 120 .....--..|||.....|.|||.|..|.|.|.||..--........|........|.|.. 4Y9H:A|PD 121 LTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAES--MRPEVASTFKVLRNVTVVLWSA 4JQ6_C 182 YPIGYAW-GYFGDGLNEDALNIVYNLADLINKAAFGLAIWAAAMK 226 180 ||.....-...................|...|..|||........ 225 4Y9H:A|PD 179 YPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 12, 37, 37, 67, 67, 97, 101, 129, 129, 158, 160, 189, 189, 226], [ 5, 30, 31, 61, 68, 98, 98, 126, 128, 157, 157, 186, 187, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'S', 'F', 'W', 'L', 'A', 'A', 'A', 'I', 'M', 'L', 'A', 'S', 'T', 'V', 'F', 'F', 'F', 'V', 'E', 'R', 'S', 'D', 'V', 'P', '-', 'V', 'K', 'W', 'K', 'T', 'S', 'L', 'T', 'V', 'A', 'G', 'L', 'V', 'T', 'G', 'V', 'A', 'F', 'W', 'H', 'Y', 'L', 'Y', 'M', 'R', 'G', 'V', 'W', 'I', 'Y', '-', '-', '-', '-', '-', '-', '-', 'A', 'G', 'E', 'T', 'P', 'T', 'V', 'F', 'R', 'Y', 'I', 'D', 'W', 'L', 'I', 'T', 'V', 'P', 'L', 'Q', 'I', 'I', 'E', 'F', 'Y', 'L', 'I', 'I', 'A', 'A', 'V', 'T', 'A', 'I', 'S', 'S', 'A', 'V', 'F', 'W', 'K', 'L', 'L', 'I', 'A', 'S', 'L', 'V', 'M', 'L', 'I', 'G', 'G', 'F', 'I', 'G', 'E', 'A', 'G', 'L', 'G', 'D', '-', '-', 'V', 'V', 'V', 'W', 'W', 'I', 'V', 'G', 'M', 'I', 'A', 'W', 'L', 'Y', 'I', 'I', 'Y', 'E', 'I', 'F', 'L', 'G', 'E', 'T', 'A', 'K', 'A', 'N', 'A', 'G', 'S', 'G', 'N', 'A', 'A', 'S', 'Q', 'Q', 'A', 'F', 'N', 'T', 'I', 'K', 'W', 'I', 'V', 'T', 'V', 'G', 'W', 'A', 'I', 'Y', 'P', 'I', 'G', 'Y', 'A', 'W', '-', 'G', 'Y', 'F', 'G', 'D', 'G', 'L', 'N', 'E', 'D', 'A', 'L', 'N', 'I', 'V', 'Y', 'N', 'L', 'A', 'D', 'L', 'I', 'N', 'K', 'A', 'A', 'F', 'G', 'L', 'A', 'I', 'W', 'A', 'A', 'A', 'M', 'K'], ['I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', '-', '-', '-', '-', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', '-', '-', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 3.9e-38, places=39) self.assertAlmostEqual(alignment.annotations["Score"], 265.93) self.assertAlmostEqual(alignment.annotations["Identities"], 24) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.298) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[6:224], "WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPF------GGEQNPIYWARYADWLFTTPLLLLDLALLVDADQG----TILALVGADGIMIGTGLVGALTKVY--SYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~l~~~~~~~~~~~i~f~~~~~~~~~~~R~~~~l~~~v~~vaal~Y~~ma~~~~~~~~~~~~~~~~~~g~~~~~~RYvdW~lTtPlll~~L~llag~~~~~~~~~~~~~i~~~~~mi~~G~~g~~~~~~~~~~~~~w~~~s~~~f~~v~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~is~~~~~i~~~ilDvl~K~~f~~~ll~~~~~ ", ) self.assertEqual(alignment.target.id, "5G28_A") self.assertEqual( alignment.target.seq[23:251], "LLTMGVGVHFAALIFFLVVSQFVAPKYRIATALSCIVMVSAGLILNSQAVMWTDAYAYVDGSYQLQDLTFSNGYRYVNWMATIPCLLLQLLIVLNLKGKELFSTATWLILAAWGMIITGYVGQLYEVDDIAQLMIWGAVSTAFFVVMNWIVGTKIFKNRATMLGGTDSTITKVFWLMMFAWTLYPIAYLVPAFMNNADGVVLRQLLFTIADISSKVIYGLMITYIAIQ", ) self.assertEqual(alignment.target.annotations["hmm_name"], "5G28_A") self.assertEqual( alignment.target.annotations["hmm_description"], "CHLORIDE PUMPING RHODOPSIN; SIGNALING PROTEIN; HET: OLA, RET; 1.57A {NONLABENS MARINUS S1-08}; Related PDB entries: 5B2N_A 5G2D_A 5G54_A 5G2C_A 5G2A_A 5FJG_A", ) self.assertEqual( alignment[0], "LLTMGVGVHFAALIFFLVVSQFVA-PKYRIATALSCIVMVSAGLILNSQAVMWTDAYAYVDGSYQLQDLTFSN-GYRYVNWMATIPCLLLQLLIVLNLKGKELFSTATWLILAAWGMIITGYVGQLYEVDDIAQLMIWGAVSTAFFVVMNWIVGTKIFKNRATMLGGTDSTITKVFWLMMFAWTLYPIAYLVPAFMNNADGVVLRQLLFTIADISSKVIYGLMITYIAIQ", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHHHGGGSCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEETTEEEECSSCCCSHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHcccccceeeeCCccccCCcccccHHHHHHHHHHHHHHHHHHHHHHccCCcchHHHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhccCCchHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 5G28_A 23 LLTMGVGVHFAALIFFLVVSQFVA-PKYRIATALSCIVMVSAGLILNSQAVMWTDAYAYV 0 .|..|..........|||....|.-|......|....|...|.....|............ 4Y9H:A|PD 6 WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPF 5G28_A 82 DGSYQLQDLTFSN-GYRYVNWMATIPCLLLQLLIVLNLKGKELFSTATWLILAAWGMIIT 60 ------.......-..||..|..|.|.|||.|.........----|...|..|...||.| 4Y9H:A|PD 66 ------GGEQNPIYWARYADWLFTTPLLLLDLALLVDADQG----TILALVGADGIMIGT 5G28_A 141 GYVGQLYEVDDIAQLMIWGAVSTAFFVVMNWIVGTKIFKNRATMLGGTDSTITKVFWLMM 120 |.||.|..|.--.....|.|.|||...................|.....||......... 4Y9H:A|PD 116 GLVGALTKVY--SYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTV 5G28_A 201 FAWTLYPIAYLVPAFMNNADGVVLRQLLFTIADISSKVIYGLMITYIAIQ 251 180 ..|..||...|...............|||...|.|.||..||........ 230 4Y9H:A|PD 174 VLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 23, 47, 47, 82, 88, 95, 95, 122, 126, 151, 153, 251], [ 6, 30, 31, 66, 66, 73, 74, 101, 101, 126, 126, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'L', 'T', 'M', 'G', 'V', 'G', 'V', 'H', 'F', 'A', 'A', 'L', 'I', 'F', 'F', 'L', 'V', 'V', 'S', 'Q', 'F', 'V', 'A', '-', 'P', 'K', 'Y', 'R', 'I', 'A', 'T', 'A', 'L', 'S', 'C', 'I', 'V', 'M', 'V', 'S', 'A', 'G', 'L', 'I', 'L', 'N', 'S', 'Q', 'A', 'V', 'M', 'W', 'T', 'D', 'A', 'Y', 'A', 'Y', 'V', 'D', 'G', 'S', 'Y', 'Q', 'L', 'Q', 'D', 'L', 'T', 'F', 'S', 'N', '-', 'G', 'Y', 'R', 'Y', 'V', 'N', 'W', 'M', 'A', 'T', 'I', 'P', 'C', 'L', 'L', 'L', 'Q', 'L', 'L', 'I', 'V', 'L', 'N', 'L', 'K', 'G', 'K', 'E', 'L', 'F', 'S', 'T', 'A', 'T', 'W', 'L', 'I', 'L', 'A', 'A', 'W', 'G', 'M', 'I', 'I', 'T', 'G', 'Y', 'V', 'G', 'Q', 'L', 'Y', 'E', 'V', 'D', 'D', 'I', 'A', 'Q', 'L', 'M', 'I', 'W', 'G', 'A', 'V', 'S', 'T', 'A', 'F', 'F', 'V', 'V', 'M', 'N', 'W', 'I', 'V', 'G', 'T', 'K', 'I', 'F', 'K', 'N', 'R', 'A', 'T', 'M', 'L', 'G', 'G', 'T', 'D', 'S', 'T', 'I', 'T', 'K', 'V', 'F', 'W', 'L', 'M', 'M', 'F', 'A', 'W', 'T', 'L', 'Y', 'P', 'I', 'A', 'Y', 'L', 'V', 'P', 'A', 'F', 'M', 'N', 'N', 'A', 'D', 'G', 'V', 'V', 'L', 'R', 'Q', 'L', 'L', 'F', 'T', 'I', 'A', 'D', 'I', 'S', 'S', 'K', 'V', 'I', 'Y', 'G', 'L', 'M', 'I', 'T', 'Y', 'I', 'A', 'I', 'Q'], ['W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', '-', '-', '-', '-', '-', '-', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', '-', '-', '-', '-', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', '-', '-', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 4e-38, places=38) self.assertAlmostEqual(alignment.annotations["Score"], 263.73) self.assertAlmostEqual(alignment.annotations["Identities"], 28) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.412) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.900) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:224], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDA----DQGTILALVGADGIMIGTGLVGALTKV-----YSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~lw~~~~~~~~~~l~f~~~~~~~~~~~R~~~~l~~~i~~vaa~~Y~~ma~~~g~~~~~~~~~~~~~~~RYvdW~~TtPlll~~l~llag~~~~~~~~~~~~lv~~~~~mi~~G~~g~~~~~~~~~~~~~~~~~f~~s~~~~~~vl~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPivw~l~~~~~g~~i~~~~~i~~~vlDv~aK~~fg~~ll~~~~~ ", ) self.assertEqual(alignment.target.id, "4HYJ_A") self.assertEqual( alignment.target.seq[7:238], "VLATQYMFWVGFVGMAAGTLYFLVERNSLAPEYRSTATVAALVTFVAAIHYYFMKDAVGTSGLLSEIDGFPTEIRYIDWLVTTPLLLVKFPLLLGLKGRLGRPLLTKLVIADVIMIVGGYIGESSINIAGGFTQLGLWSYLIGCFAWIYIIYLLFTNVTKAAENKPAPIRDALLKMRLFILIGWAIYPIGYAVTLFAPGVEIQLVRELIYNFADLTNKVGFGLIAFFAVKT", ) self.assertEqual(alignment.target.annotations["hmm_name"], "4HYJ_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Rhodopsin; Seven-helical transmembrane protein, Proton pump; HET: RET, LFA; 2.3A {Exiguobacterium sibiricum} SCOP: f.13.1.0; Related PDB entries: 4HYJ_B", ) self.assertEqual( alignment[0], "VLATQYMFWVGFVGMAAGTLYFLVERNSLA-PEYRSTATVAALVTFVAAIHYYFMKDAVGTSGLLSEIDGFPT-EIRYIDWLVTTPLLLVKFPLLLGLKGRLGRPLLTKLVIADVIMIVGGYIGESSINIAGGFTQLGLWSYLIGCFAWIYIIYLLFTNVTKAAENKPAPIRDALLKMRLFILIGWAIYPIGYAVTLFAPGVEIQLVRELIYNFADLTNKVGFGLIAFFAVKT", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHHHHHHHHSGGGSCTTTHHHHHHHHHHHHHHHHHHHHHHHHHCSSCCGGGCCSCHHHHHHHHHHHHHHHHHTHHHHHHCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHTTSCHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " hHHHHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccccCCCCcHHHHhHHHhHHHHHHHHHHHHHccccccCHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHh ", ) self.assertEqual( str(alignment), """\ 4HYJ_A 7 VLATQYMFWVGFVGMAAGTLYFLVERNSLA-PEYRSTATVAALVTFVAAIHYYFMKDAVG 0 ..........|...|..|||||||......-|..........||...|...|..|....| 4Y9H:A|PD 0 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG 4HYJ_A 66 TSGLLSEIDGFPT-EIRYIDWLVTTPLLLVKFPLLLGLKGRLGRPLLTKLVIADVIMIVG 60 ...........|.-..||.|||.||||||....||...----.......||.||.|||.. 4Y9H:A|PD 60 LTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDA----DQGTILALVGADGIMIGT 4HYJ_A 125 GYIGESSINIAGGFTQLGLWSYLIGCFAWIYIIYLLFTNVTKAAENKPAPIRDALLKMRL 120 |..|.....-----.........|...|..||.|.||...|..||.............|. 4Y9H:A|PD 116 GLVGALTKV-----YSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRN 4HYJ_A 185 FILIGWAIYPIGYAVTLFAPGVEIQLVRELIYNFADLTNKVGFGLIAFFAVKT 238 180 .....|..||..........|........|.....|...|||||||....... 233 4Y9H:A|PD 171 VTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 7, 37, 37, 79, 79, 103, 107, 134, 139, 238], [ 0, 30, 31, 73, 74, 98, 98, 125, 125, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['V', 'L', 'A', 'T', 'Q', 'Y', 'M', 'F', 'W', 'V', 'G', 'F', 'V', 'G', 'M', 'A', 'A', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'E', 'R', 'N', 'S', 'L', 'A', '-', 'P', 'E', 'Y', 'R', 'S', 'T', 'A', 'T', 'V', 'A', 'A', 'L', 'V', 'T', 'F', 'V', 'A', 'A', 'I', 'H', 'Y', 'Y', 'F', 'M', 'K', 'D', 'A', 'V', 'G', 'T', 'S', 'G', 'L', 'L', 'S', 'E', 'I', 'D', 'G', 'F', 'P', 'T', '-', 'E', 'I', 'R', 'Y', 'I', 'D', 'W', 'L', 'V', 'T', 'T', 'P', 'L', 'L', 'L', 'V', 'K', 'F', 'P', 'L', 'L', 'L', 'G', 'L', 'K', 'G', 'R', 'L', 'G', 'R', 'P', 'L', 'L', 'T', 'K', 'L', 'V', 'I', 'A', 'D', 'V', 'I', 'M', 'I', 'V', 'G', 'G', 'Y', 'I', 'G', 'E', 'S', 'S', 'I', 'N', 'I', 'A', 'G', 'G', 'F', 'T', 'Q', 'L', 'G', 'L', 'W', 'S', 'Y', 'L', 'I', 'G', 'C', 'F', 'A', 'W', 'I', 'Y', 'I', 'I', 'Y', 'L', 'L', 'F', 'T', 'N', 'V', 'T', 'K', 'A', 'A', 'E', 'N', 'K', 'P', 'A', 'P', 'I', 'R', 'D', 'A', 'L', 'L', 'K', 'M', 'R', 'L', 'F', 'I', 'L', 'I', 'G', 'W', 'A', 'I', 'Y', 'P', 'I', 'G', 'Y', 'A', 'V', 'T', 'L', 'F', 'A', 'P', 'G', 'V', 'E', 'I', 'Q', 'L', 'V', 'R', 'E', 'L', 'I', 'Y', 'N', 'F', 'A', 'D', 'L', 'T', 'N', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'A', 'F', 'F', 'A', 'V', 'K', 'T'], ['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', '-', '-', '-', '-', 'D', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', '-', '-', '-', '-', '-', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 4.4e-38, places=39) self.assertAlmostEqual(alignment.annotations["Score"], 263.83) self.assertAlmostEqual(alignment.annotations["Identities"], 27) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.383) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.700) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:224], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDAD----QGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFG-FTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIG-SEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~lw~~~~~~~~~~~~f~~~~~~~~~~~R~~~~l~~~i~~ia~~aY~~ma~~~~~~g~~~~~~RYvdW~lTtPlll~~l~llag~~~~~~~~~~~~lv~~~~~Mi~~G~~g~~~~~~~w~~f~~g~~~f~~il~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~eg~~~i~~~~e~i~y~ilDv~~K~~fg~~l~~~~~~ ", ) self.assertEqual(alignment.target.id, "4KNF_D") self.assertEqual( alignment.target.seq[26:246], "SDTVGVSFWLVTAGMLAATVFFFVERDQVSAKWKTSLTVSGLITGIAFWHYLYMRGVWIDTGDTPTVFRYINWLLTVPLLVVEFYLILAACTSVAASLFKKLLAGSLVMLGAGFAGEAGLAPVLPAFIIGMAGWLYMIYELYMGEGKAAVSTASPAVNSAYNAMMMIIVVGWAIYPAGYAAGYLMGGEGVYASNLNLIYNLADFVNKILFGLIIWNVAVK", ) self.assertEqual(alignment.target.annotations["hmm_name"], "4KNF_D") self.assertEqual( alignment.target.annotations["hmm_description"], "Blue-light absorbing proteorhodopsin; Membrane, Proton transport, ion transport; HET: RET; 2.6A {gamma proteobacterium 'Hot 75m4'} SCOP: l.1.1.1, f.13.1.0; Related PDB entries: 2L6X_A 4KNF_A 4KNF_B 4KNF_C 4KNF_E 4KLY_A 4KLY_B 4KLY_E 4KLY_C 4KLY_D", ) self.assertEqual( alignment[0], "SDTVGVSFWLVTAGMLAATVFFFVERDQVS-AKWKTSLTVSGLITGIAFWHYLYMRGVWID-------TGDTPTVFRYINWLLTVPLLVVEFYLILAACTSVAASLFKKLLAGSLVMLGAGFAGEAGLA--PVLPAFIIGMAGWLYMIYELYMGEGKAAVSTASPAVNSAYNAMMMIIVVGWAIYPAGYAAGYLMGGEGVYASNLNLIYNLADFVNKILFGLIIWNVAVK", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " SCHHHHHHHHHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHSTTSCCCCCSSHHHHHHHHHHCCCCCTTHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " chHHHHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHhHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHhhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 4KNF_D 26 SDTVGVSFWLVTAGMLAATVFFFVERDQVS-AKWKTSLTVSGLITGIAFWHYLYMRGVWI 0 .........|.||.|...|..|.|....||-...|.......|...|||..||.|..... 4Y9H:A|PD 0 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG 4KNF_D 85 D-------TGDTPTVFRYINWLLTVPLLVVEFYLILAACTSVAASLFKKLLAGSLVMLGA 60 .-------........||..||.|.|||.....|...|.----......|......|.|. 4Y9H:A|PD 60 LTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDAD----QGTILALVGADGIMIGT 4KNF_D 138 GFAGEAGLA--PVLPAFIIGMAGWLYMIYELYMGEGKAAVSTASPAVNSAYNAMMMIIVV 120 |..|.....--.......|..|..||..|.|..|-.........|.|.|.........|| 4Y9H:A|PD 116 GLVGALTKVYSYRFVWWAISTAAMLYILYVLFFG-FTSKAESMRPEVASTFKVLRNVTVV 4KNF_D 196 GWAIYPAGYAAGYLMGGEGVYASNLNLIYNLADFVNKILFGLIIWNVAVK 246 180 .|..||.....|-..|...|......|.....|...|..||||....... 230 4Y9H:A|PD 175 LWSAYPVVWLIG-SEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 26, 56, 56, 86, 86, 117, 121, 147, 147, 170, 171, 208, 209, 246], [ 0, 30, 31, 61, 68, 99, 99, 125, 127, 150, 150, 187, 187, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['S', 'D', 'T', 'V', 'G', 'V', 'S', 'F', 'W', 'L', 'V', 'T', 'A', 'G', 'M', 'L', 'A', 'A', 'T', 'V', 'F', 'F', 'F', 'V', 'E', 'R', 'D', 'Q', 'V', 'S', '-', 'A', 'K', 'W', 'K', 'T', 'S', 'L', 'T', 'V', 'S', 'G', 'L', 'I', 'T', 'G', 'I', 'A', 'F', 'W', 'H', 'Y', 'L', 'Y', 'M', 'R', 'G', 'V', 'W', 'I', 'D', '-', '-', '-', '-', '-', '-', '-', 'T', 'G', 'D', 'T', 'P', 'T', 'V', 'F', 'R', 'Y', 'I', 'N', 'W', 'L', 'L', 'T', 'V', 'P', 'L', 'L', 'V', 'V', 'E', 'F', 'Y', 'L', 'I', 'L', 'A', 'A', 'C', 'T', 'S', 'V', 'A', 'A', 'S', 'L', 'F', 'K', 'K', 'L', 'L', 'A', 'G', 'S', 'L', 'V', 'M', 'L', 'G', 'A', 'G', 'F', 'A', 'G', 'E', 'A', 'G', 'L', 'A', '-', '-', 'P', 'V', 'L', 'P', 'A', 'F', 'I', 'I', 'G', 'M', 'A', 'G', 'W', 'L', 'Y', 'M', 'I', 'Y', 'E', 'L', 'Y', 'M', 'G', 'E', 'G', 'K', 'A', 'A', 'V', 'S', 'T', 'A', 'S', 'P', 'A', 'V', 'N', 'S', 'A', 'Y', 'N', 'A', 'M', 'M', 'M', 'I', 'I', 'V', 'V', 'G', 'W', 'A', 'I', 'Y', 'P', 'A', 'G', 'Y', 'A', 'A', 'G', 'Y', 'L', 'M', 'G', 'G', 'E', 'G', 'V', 'Y', 'A', 'S', 'N', 'L', 'N', 'L', 'I', 'Y', 'N', 'L', 'A', 'D', 'F', 'V', 'N', 'K', 'I', 'L', 'F', 'G', 'L', 'I', 'I', 'W', 'N', 'V', 'A', 'V', 'K'], ['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', '-', '-', '-', '-', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', '-', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', '-', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 6.6e-38, places=39) self.assertAlmostEqual(alignment.annotations["Score"], 263.77) self.assertAlmostEqual(alignment.annotations["Identities"], 27) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.402) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.900) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[7:224], "LALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "LALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSML-LGYGLTMVPFG----GEQNPIYWARYADWLFTTPLLLLDLALLVDAD----QGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAES--MRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEG-AGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~~~~~~~~f~~~~~~~~~~~r~~~~l~~~i~~va~~~Y~~ma~~~~g~~~~~~g~~~~~g~~~~~~~RYv~W~~TtPlll~~l~ll~g~~~~~~~~~~~~~i~~~~~mi~~G~~g~~~~~~~~~~~w~~is~~~f~~vl~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~~~~g~i~~~~~~i~y~vlDv~~K~~f~~~l~~~~~~ ", ) self.assertEqual(alignment.target.id, "5AZD_C") self.assertEqual( alignment.target.seq[18:246], "LSLTIAGMLAAFVFFLLARSYVAPRYHIALYLSALIVFIAGYHYLRIFESWVGAYQLQDGVYVPTGKPFNDFYRYADWLLTVPLLLLELILVLGLTAARTWNLSIKLVVASVLMLALGYVGEVNTEPGPRTLWGALSSIPFFYILYVLWVELGQAIREAKFGPRVLELLGATRLVLLMSWGFYPIAYALGTWLPGGAAQEVAIQIGYSLADLIAXPIYGLLVFAIARA", ) self.assertEqual(alignment.target.annotations["hmm_name"], "5AZD_C") self.assertEqual( alignment.target.annotations["hmm_description"], "Thermophilic rhodopsin; Membrane protein, Retinal, Ion pump; HET: LYR; 2.8A {Thermus thermophilus JL-18}; Related PDB entries: 5AZD_D 5AZD_B 5AZD_A", ) self.assertEqual( alignment[0], "LSLTIAGMLAAFVFFLLARSYVA-PRYHIALYLSALIVFIAGYHYLRIFESWVGAYQLQDGVYVPTGKPFNDFYRYADWLLTVPLLLLELILVLGLTAARTWNLSIKLVVASVLMLALGYVGEVNTEPGPRTLWGALSSIPFFYILYVLWVELGQAIREAKFGPRVLELLGATRLVLLMSWGFYPIAYALGTWLPGGAAQEVAIQIGYSLADLIAXPIYGLLVFAIARA", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHGGGGSCGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEETTEEEECSCCCCCCCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHSCCSHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHTHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHHHHHHHhcccceeccCCcccCCCceeccHHHHHHHHHHHHHHHHHHHHHHccchhccHHHHHHHHHHHHHHHHhHHHHHhCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHhcHHHHHHHHHHHHHh ", ) self.assertEqual( str(alignment), """\ 5AZD_C 18 LSLTIAGMLAAFVFFLLARSYVA-PRYHIALYLSALIVFIAGYHYLRIFESWVGAYQLQD 0 |.|..|.|......||.....|.-|..........|...||...||...-...|...... 4Y9H:A|PD 7 LALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSML-LGYGLTMVPF 5AZD_C 77 GVYVPTGKPFNDFYRYADWLLTVPLLLLELILVLGLTAARTWNLSIKLVVASVLMLALGY 60 |----.........||||||.|.|||||.|.|.....----......||.|...|...|. 4Y9H:A|PD 66 G----GEQNPIYWARYADWLFTTPLLLLDLALLVDAD----QGTILALVGADGIMIGTGL 5AZD_C 137 VGEVNTEPGPRTLWGALSSIPFFYILYVLWVELGQAIREAKFGPRVLELLGATRLVLLMS 120 ||........|..|.|.|.....||||||..........--..|.|.......|.|.... 4Y9H:A|PD 118 VGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAES--MRPEVASTFKVLRNVTVVL 5AZD_C 197 WGFYPIAYALGTWLPGGAAQEVAIQIGYSLADLIAXPIYGLLVFAIARA 246 180 |..||.....|...-.|..............|..|....||........ 229 4Y9H:A|PD 176 WSAYPVVWLIGSEG-AGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 18, 41, 41, 66, 67, 78, 82, 114, 118, 176, 178, 211, 212, 246], [ 7, 30, 31, 56, 56, 67, 67, 99, 99, 157, 157, 190, 190, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'S', 'L', 'T', 'I', 'A', 'G', 'M', 'L', 'A', 'A', 'F', 'V', 'F', 'F', 'L', 'L', 'A', 'R', 'S', 'Y', 'V', 'A', '-', 'P', 'R', 'Y', 'H', 'I', 'A', 'L', 'Y', 'L', 'S', 'A', 'L', 'I', 'V', 'F', 'I', 'A', 'G', 'Y', 'H', 'Y', 'L', 'R', 'I', 'F', 'E', 'S', 'W', 'V', 'G', 'A', 'Y', 'Q', 'L', 'Q', 'D', 'G', 'V', 'Y', 'V', 'P', 'T', 'G', 'K', 'P', 'F', 'N', 'D', 'F', 'Y', 'R', 'Y', 'A', 'D', 'W', 'L', 'L', 'T', 'V', 'P', 'L', 'L', 'L', 'L', 'E', 'L', 'I', 'L', 'V', 'L', 'G', 'L', 'T', 'A', 'A', 'R', 'T', 'W', 'N', 'L', 'S', 'I', 'K', 'L', 'V', 'V', 'A', 'S', 'V', 'L', 'M', 'L', 'A', 'L', 'G', 'Y', 'V', 'G', 'E', 'V', 'N', 'T', 'E', 'P', 'G', 'P', 'R', 'T', 'L', 'W', 'G', 'A', 'L', 'S', 'S', 'I', 'P', 'F', 'F', 'Y', 'I', 'L', 'Y', 'V', 'L', 'W', 'V', 'E', 'L', 'G', 'Q', 'A', 'I', 'R', 'E', 'A', 'K', 'F', 'G', 'P', 'R', 'V', 'L', 'E', 'L', 'L', 'G', 'A', 'T', 'R', 'L', 'V', 'L', 'L', 'M', 'S', 'W', 'G', 'F', 'Y', 'P', 'I', 'A', 'Y', 'A', 'L', 'G', 'T', 'W', 'L', 'P', 'G', 'G', 'A', 'A', 'Q', 'E', 'V', 'A', 'I', 'Q', 'I', 'G', 'Y', 'S', 'L', 'A', 'D', 'L', 'I', 'A', 'X', 'P', 'I', 'Y', 'G', 'L', 'L', 'V', 'F', 'A', 'I', 'A', 'R', 'A'], ['L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', '-', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', '-', '-', '-', '-', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', '-', '-', '-', '-', 'Q', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', '-', '-', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', '-', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 7e-38, places=38) self.assertAlmostEqual(alignment.annotations["Score"], 264.24) self.assertAlmostEqual(alignment.annotations["Identities"], 22) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.378) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.800) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[6:224], "WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGG---EQNPIYW--ARYADWLFTTPLLLLDLALLVDADQGT----ILALVGADGIMIGTGLVGALTKVY---SYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSE---GAGIVPL---NIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~w~~~~~m~~~~l~f~~~~~~~~~~~R~~~~l~~~i~~va~~~Y~~m~~~~~~~~~~~~g~~~~~~~~~~~~~RYvdW~iTtPlll~~l~llag~~~~~~~~~~~~~v~~~~~mi~~g~~~~~~~~~~~~~~~~~w~~is~~~~~~il~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~~~~~~~~~~~~~~~~e~i~y~ilDv~~K~~fg~~ll~~~~~ ", ) self.assertEqual(alignment.target.id, "3DDL_A") self.assertEqual( alignment.target.seq[18:253], "MFSFTVATMTASFVFFVLARNNVAPKYRISMMVSALVVFIAGYHYFRITSSWEAAYALQNGMYQPTGELFNDAYRYVDWLLTVPLLTVELVLVMGLPKNERGPLAAKLGFLAALMIVLGYPGEVSENAALFGTRGLWGFLSTIPFVWILYILFTQLGDTIQRQSSRVSTLLGNARLLLLATWGFYPIAYMIPMAFPEAFPSNTPGTIVALQVGYTIADVLAKAGYGVLIYNIAKA", ) self.assertEqual(alignment.target.annotations["hmm_name"], "3DDL_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Xanthorhodopsin; rhodopsin, carotenoid, ion pump, light-harvesting; HET: PX4, SXN, PCW, RET, UNL; 1.9A {Salinibacter ruber} SCOP: f.13.1.0; Related PDB entries: 3DDL_B", ) self.assertEqual( alignment[0], "MFSFTVATMTASFVFFVLARNNVA-PKYRISMMVSALVVFIAGYHYFRITSSWEAAYALQNGMYQPTGELFNDAYRYVDWLLTVPLLTVELVLVMGLPKNERGPLAAKLGFLAALMIVLGYPGEVSENAALFGTRGLWGFLSTIPFVWILYILFTQLGDTIQRQSSRVSTLLGNARLLLLATWGFYPIAYMIPMAFPEAFPSNTPGTIVALQVGYTIADVLAKAGYGVLIYNIAKA", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHHGGGGSCGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHTEEECSSSEEECSCCCCCHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTCSCCCTTSHHHHHHHHHHHHHHHHHHHHHHSCHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCTTCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHHHHHHHHHHhchHhHHHhhCCCCCCCCcccchHHHHHHHHHHHHHHHHHHHHHhCCCcccchhHHHHHHHHHHHHHHhchHHHhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 3DDL_A 18 MFSFTVATMTASFVFFVLARNNVA-PKYRISMMVSALVVFIAGYHYFRITSSWEAAYALQ 0 ......|.|......|......|.-|..........||..||...|.............. 4Y9H:A|PD 6 WLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPF 3DDL_A 77 NGMYQPTGELFNDAYRYVDWLLTVPLLTVELVLVMGLPKNERGPLAAKLGFLAALMIVLG 60 .|---.......--.||.|||.|.|||...|.|........----...|......||..| 4Y9H:A|PD 66 GG---EQNPIYW--ARYADWLFTTPLLLLDLALLVDADQGT----ILALVGADGIMIGTG 3DDL_A 137 YPGEVSENAALFGTRGLWGFLSTIPFVWILYILFTQLGDTIQRQSSRVSTLLGNARLLLL 120 ..|......---..|..|...||.....|||.||.............|.......|.... 4Y9H:A|PD 117 LVGALTKVY---SYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTV 3DDL_A 197 ATWGFYPIAYMIPMAFPEAFPSNTPGTIVALQVGYTIADVLAKAGYGVLIYNIAKA 253 180 ..|..||....|...---.......---..........||.||.|.|......... 236 4Y9H:A|PD 174 VLWSAYPVVWLIGSE---GAGIVPL---NIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 18, 42, 42, 79, 82, 89, 91, 118, 122, 146, 149, 212, 215, 222, 225, 253], [ 6, 30, 31, 68, 68, 75, 75, 102, 102, 126, 126, 189, 189, 196, 196, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['M', 'F', 'S', 'F', 'T', 'V', 'A', 'T', 'M', 'T', 'A', 'S', 'F', 'V', 'F', 'F', 'V', 'L', 'A', 'R', 'N', 'N', 'V', 'A', '-', 'P', 'K', 'Y', 'R', 'I', 'S', 'M', 'M', 'V', 'S', 'A', 'L', 'V', 'V', 'F', 'I', 'A', 'G', 'Y', 'H', 'Y', 'F', 'R', 'I', 'T', 'S', 'S', 'W', 'E', 'A', 'A', 'Y', 'A', 'L', 'Q', 'N', 'G', 'M', 'Y', 'Q', 'P', 'T', 'G', 'E', 'L', 'F', 'N', 'D', 'A', 'Y', 'R', 'Y', 'V', 'D', 'W', 'L', 'L', 'T', 'V', 'P', 'L', 'L', 'T', 'V', 'E', 'L', 'V', 'L', 'V', 'M', 'G', 'L', 'P', 'K', 'N', 'E', 'R', 'G', 'P', 'L', 'A', 'A', 'K', 'L', 'G', 'F', 'L', 'A', 'A', 'L', 'M', 'I', 'V', 'L', 'G', 'Y', 'P', 'G', 'E', 'V', 'S', 'E', 'N', 'A', 'A', 'L', 'F', 'G', 'T', 'R', 'G', 'L', 'W', 'G', 'F', 'L', 'S', 'T', 'I', 'P', 'F', 'V', 'W', 'I', 'L', 'Y', 'I', 'L', 'F', 'T', 'Q', 'L', 'G', 'D', 'T', 'I', 'Q', 'R', 'Q', 'S', 'S', 'R', 'V', 'S', 'T', 'L', 'L', 'G', 'N', 'A', 'R', 'L', 'L', 'L', 'L', 'A', 'T', 'W', 'G', 'F', 'Y', 'P', 'I', 'A', 'Y', 'M', 'I', 'P', 'M', 'A', 'F', 'P', 'E', 'A', 'F', 'P', 'S', 'N', 'T', 'P', 'G', 'T', 'I', 'V', 'A', 'L', 'Q', 'V', 'G', 'Y', 'T', 'I', 'A', 'D', 'V', 'L', 'A', 'K', 'A', 'G', 'Y', 'G', 'V', 'L', 'I', 'Y', 'N', 'I', 'A', 'K', 'A'], ['W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', '-', '-', '-', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', '-', '-', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', '-', '-', '-', '-', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', '-', '-', '-', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', '-', '-', '-', 'G', 'A', 'G', 'I', 'V', 'P', 'L', '-', '-', '-', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 6.1e-37, places=38) self.assertAlmostEqual(alignment.annotations["Score"], 263.90) self.assertAlmostEqual(alignment.annotations["Identities"], 20) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.322) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 6.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[4:224], "WIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "WIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTL-VPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQG---TILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMR-PEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~W~~f~v~~l~~l~f~~~~~r~~~~~r~~y~~~~~~i~~iiaY~~ma~~~g~~~~~~gr~v~~~RYvdWllTtPLlL~~L~llag~~~~~~~~i~~li~~d~~MIvtGl~gal~~~~~kw~~f~ig~~~~l~~~~~~~~~~~~~a~~~~~~~~~~~~~~L~~~~~v~W~~YPIvwlL~~eG~~~is~~~e~i~y~ilDilaK~~fg~ll~~~r~~ ", ) self.assertEqual(alignment.target.id, "3UG9_A") self.assertEqual( alignment.target.seq[68:286], "NILQWITFALSALCLMFYGYQTWKSTCGWEEIYVATIEMIKFIIEYFHEFDEPAVIYSSNGNKTVWLRYAEWLLTCPVILIHLSNLTGLANDYNKRTMGLLVSDIGTIVWGTTAALSKGYVRVIFFLMGLCYGIYTFFNAAKVYIEAYHTVPKGRCRQVVTGMAWLFFVSWGMFPILFILGPEGFGVLSVYGSTVGHTIIDLMSKNCWGLLGHYLRVL", ) self.assertEqual(alignment.target.annotations["hmm_name"], "3UG9_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Archaeal-type opsin 1, Archaeal-type opsin; microbialrhodopsin, seven-transmembrane, light-gated cation channel; HET: OLA, RET; 2.3A {Chlamydomonas reinhardtii}; Related PDB entries: 6CSO_A 6EIG_A 6EIG_B 6EID_B 6EID_A 4YZI_A 6CSN_A", ) self.assertEqual( alignment[0], "NILQWITFALSALCLMFYGYQTWKST-CGWEEIYVATIEMIKFI--IEYFHEFDEPAVIYSS---NGNKTVWLRYAEWLLTCPVILIHLSNLTGLANDYNKRTMGLLVSDIGTIVWGTTAALSKG-YVRVIFFLMGLCYGIYTFFNAAKVYIEAYHTVPKGRCRQVVTGMAWLFFVSWGMFPILFILGPEGFGVLSVYGSTVGHTIIDLMSKNCWGLLGHYLRVL", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHTTSTTTSEECTTSCEECHHHHHHHHHHHHHHHHHHTTTTSCCCCCCHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCSSCHHHHHHHHHHHHCCCCCCHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHhcCCceeecCCCceeeHHHHHHHHhHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHHHHHHHHHHcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 3UG9_A 68 NILQWITFALSALCLMFYGYQTWKST-CGWEEIYVATIEMIKFI--IEYFHEFDEPAVIY 0 .|......||..|.............-......|..|..-...|--..|........... 4Y9H:A|PD 4 WIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTL-VPAIAFTMYLSMLLGYGLTM 3UG9_A 125 SS---NGNKTVWLRYAEWLLTCPVILIHLSNLTGLANDYNKRTMGLLVSDIGTIVWGTTA 60 ..---..|...|.|||.||.|.|..|..|..|......---....|...|...|..|... 4Y9H:A|PD 63 VPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQG---TILALVGADGIMIGTGLVG 3UG9_A 182 ALSKG-YVRVIFFLMGLCYGIYTFFNAAKVYIEAYHTVPKGRCRQVVTGMAWLFFVSWGM 120 ||.|.-..|............|.................-...............|.|.. 4Y9H:A|PD 120 ALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMR-PEVASTFKVLRNVTVVLWSA 3UG9_A 241 FPILFILGPEGFGVLSVYGSTVGHTIIDLMSKNCWGLLGHYLRVL 286 180 .|.....|.||.|.......|......|...|...||.....|.. 225 4Y9H:A|PD 179 YPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 68, 94, 94, 106, 107, 111, 111, 127, 127, 160, 163, 187, 187, 220, 221, 286], [ 4, 30, 31, 43, 43, 47, 49, 65, 68, 101, 101, 125, 126, 159, 159, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['N', 'I', 'L', 'Q', 'W', 'I', 'T', 'F', 'A', 'L', 'S', 'A', 'L', 'C', 'L', 'M', 'F', 'Y', 'G', 'Y', 'Q', 'T', 'W', 'K', 'S', 'T', '-', 'C', 'G', 'W', 'E', 'E', 'I', 'Y', 'V', 'A', 'T', 'I', 'E', 'M', 'I', 'K', 'F', 'I', '-', '-', 'I', 'E', 'Y', 'F', 'H', 'E', 'F', 'D', 'E', 'P', 'A', 'V', 'I', 'Y', 'S', 'S', '-', '-', '-', 'N', 'G', 'N', 'K', 'T', 'V', 'W', 'L', 'R', 'Y', 'A', 'E', 'W', 'L', 'L', 'T', 'C', 'P', 'V', 'I', 'L', 'I', 'H', 'L', 'S', 'N', 'L', 'T', 'G', 'L', 'A', 'N', 'D', 'Y', 'N', 'K', 'R', 'T', 'M', 'G', 'L', 'L', 'V', 'S', 'D', 'I', 'G', 'T', 'I', 'V', 'W', 'G', 'T', 'T', 'A', 'A', 'L', 'S', 'K', 'G', '-', 'Y', 'V', 'R', 'V', 'I', 'F', 'F', 'L', 'M', 'G', 'L', 'C', 'Y', 'G', 'I', 'Y', 'T', 'F', 'F', 'N', 'A', 'A', 'K', 'V', 'Y', 'I', 'E', 'A', 'Y', 'H', 'T', 'V', 'P', 'K', 'G', 'R', 'C', 'R', 'Q', 'V', 'V', 'T', 'G', 'M', 'A', 'W', 'L', 'F', 'F', 'V', 'S', 'W', 'G', 'M', 'F', 'P', 'I', 'L', 'F', 'I', 'L', 'G', 'P', 'E', 'G', 'F', 'G', 'V', 'L', 'S', 'V', 'Y', 'G', 'S', 'T', 'V', 'G', 'H', 'T', 'I', 'I', 'D', 'L', 'M', 'S', 'K', 'N', 'C', 'W', 'G', 'L', 'L', 'G', 'H', 'Y', 'L', 'R', 'V', 'L'], ['W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', '-', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', '-', '-', '-', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', '-', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 1e-36, places=37) self.assertAlmostEqual(alignment.annotations["Score"], 249.63) self.assertAlmostEqual(alignment.annotations["Identities"], 23) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.407) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.300) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[5:224], "IWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "IWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQG---TILALVGADGIMIGTGLVGALTKV-YSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~w~~~~~~~~~~~~f~~~~~~~~~~~R~~~~l~~~i~~ia~~~Y~~m~~~~~~g~~~~~~RYv~W~~TtPlll~~l~~l~g~~~~~~~~~~~~~~~~~~mi~~g~~g~~~~~~~~~~w~~~~~s~~~~~~ll~~l~~~~~~~~~~~~~~~~~l~~~~~~~W~~YPivw~l~~~g~~~~~~~~~~~~~Di~~K~~f~~~ll~~~~~ ", ) self.assertEqual(alignment.target.id, "5JSI_A") self.assertEqual( alignment.target.seq[6:213], "RLFMVATVGMLAGTVFLLASSREVKPEHRRGVYISALVCGIAWYHYQKMGASWESGSYDTGLRYVDWVLTVPLMFVEVLAVTRKGAAYNEAVRNWGIAATVMIGAGYYGETSAAGSNEYWTGFVIAMATYVWLMRNLQAEGEGLKGDQAVAFENIKNLILVGWIIYPLGYIAPVVGDFDAIREVLYTIADIINXVGLGVLVLQMARV", ) self.assertEqual(alignment.target.annotations["hmm_name"], "5JSI_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Nitrate/nitrite sensor protein NarQ (E.C.2.7.13.3); membrane protein, iodide, UNKNOWN FUNCTION; HET: LYR, OLC, LFA, IOD; 2.0A {Candidatus Actinomarina minuta}; Related PDB entries: 5JSI_B", ) self.assertEqual( alignment[0], "RLFMVATVGMLAGTVFLLASSREVK-PEHRRGVYISALVCGIAWYHYQKMGASWE--------SGSYDTGLRYVDWVLTVPLMFVEVLAVTRKGAAYNEAVRNWGIAATVMIGAGYYGETSAAGSNEYWTGFVIAMATYVWLMRNLQA----EGEGLKGDQAVAFENIKNLILVGWIIYPLGYIAPVVG--DFD-AIREVLYTIADIINXVGLGVLVLQMARV", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHHHHGGGSCGGGCHHHHHHHHHHHHHHHHHHHHHHHHHHSSCCTHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHHHHHHHHHHHHHHHHTTTTCCHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcHHHHhHHHhHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCChHHHHHHHHHHHHHHhHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 5JSI_A 6 RLFMVATVGMLAGTVFLLASSREVK-PEHRRGVYISALVCGIAWYHYQKMGASWE----- 0 ......|..|..||...|.....|.-|.......|..||..||...|..|.....----- 4Y9H:A|PD 5 IWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVP 5JSI_A 60 ---SGSYDTGLRYVDWVLTVPLMFVEVLAVTRKGAAYNEAVRNWGIAATVMIGAGYYGET 60 ---........||.||..|.||..............---.......|...|||.|..|.. 4Y9H:A|PD 65 FGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQG---TILALVGADGIMIGTGLVGAL 5JSI_A 117 SAAGSNEYWTGFVIAMATYVWLMRNLQA----EGEGLKGDQAVAFENIKNLILVGWIIYP 120 ...-.........|..|........|..----..|......|..|....|...|.|..|| 4Y9H:A|PD 122 TKV-YSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYP 5JSI_A 173 LGYIAPVVG--DFD-AIREVLYTIADIINXVGLGVLVLQMARV 213 180 ........|--...-.|...|....|....||.|...|..... 223 4Y9H:A|PD 181 VVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 6, 31, 31, 60, 60, 93, 96, 120, 121, 145, 145, 182, 182, 185, 185, 213], [ 5, 30, 31, 60, 68, 101, 101, 125, 125, 149, 153, 190, 192, 195, 196, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'L', 'F', 'M', 'V', 'A', 'T', 'V', 'G', 'M', 'L', 'A', 'G', 'T', 'V', 'F', 'L', 'L', 'A', 'S', 'S', 'R', 'E', 'V', 'K', '-', 'P', 'E', 'H', 'R', 'R', 'G', 'V', 'Y', 'I', 'S', 'A', 'L', 'V', 'C', 'G', 'I', 'A', 'W', 'Y', 'H', 'Y', 'Q', 'K', 'M', 'G', 'A', 'S', 'W', 'E', '-', '-', '-', '-', '-', '-', '-', '-', 'S', 'G', 'S', 'Y', 'D', 'T', 'G', 'L', 'R', 'Y', 'V', 'D', 'W', 'V', 'L', 'T', 'V', 'P', 'L', 'M', 'F', 'V', 'E', 'V', 'L', 'A', 'V', 'T', 'R', 'K', 'G', 'A', 'A', 'Y', 'N', 'E', 'A', 'V', 'R', 'N', 'W', 'G', 'I', 'A', 'A', 'T', 'V', 'M', 'I', 'G', 'A', 'G', 'Y', 'Y', 'G', 'E', 'T', 'S', 'A', 'A', 'G', 'S', 'N', 'E', 'Y', 'W', 'T', 'G', 'F', 'V', 'I', 'A', 'M', 'A', 'T', 'Y', 'V', 'W', 'L', 'M', 'R', 'N', 'L', 'Q', 'A', '-', '-', '-', '-', 'E', 'G', 'E', 'G', 'L', 'K', 'G', 'D', 'Q', 'A', 'V', 'A', 'F', 'E', 'N', 'I', 'K', 'N', 'L', 'I', 'L', 'V', 'G', 'W', 'I', 'I', 'Y', 'P', 'L', 'G', 'Y', 'I', 'A', 'P', 'V', 'V', 'G', '-', '-', 'D', 'F', 'D', '-', 'A', 'I', 'R', 'E', 'V', 'L', 'Y', 'T', 'I', 'A', 'D', 'I', 'I', 'N', 'X', 'V', 'G', 'L', 'G', 'V', 'L', 'V', 'L', 'Q', 'M', 'A', 'R', 'V'], ['I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', '-', '-', '-', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', '-', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 2.7e-36, places=37) self.assertAlmostEqual(alignment.annotations["Score"], 255.00) self.assertAlmostEqual(alignment.annotations["Identities"], 21) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.325) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.700) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:224], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQ---GTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFG-------FTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~g~~~~w~v~~~~~~~~~~~~~sr~~~~~~l~~~i~~va~~~Y~~ma~g~g~~~~~~~r~v~~~RYv~W~vTtPlll~~l~llag~~~~~~~~~~~~i~~~~~mi~~G~~g~~~~~~~~kw~~~~is~~~fl~v~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~G~~~is~~~e~i~y~ilDil~K~~f~~~ll~~~~~ ", ) self.assertEqual(alignment.target.id, "6CSM_D") self.assertEqual( alignment.target.seq[26:248], "DGIKYVQLVMAVVSACQVFFMVTRAPKVPWEAIYLPTTEMITYSLAFTGNGYIRVANGKYLPWARMASWLCTCPIMLGLVSNMALVKYKSIPLNPMMIAASSICTVFGITASVVLDPLHVWLYCFISSIFFIFEMVVAFAIFAITIHDFQTIGSPMSLKVVERLKLMRIVFYVSWMAYPILWSFSSTGACIMSENTSSVLYLLGDALCKNTYGILLWATTWG", ) self.assertEqual(alignment.target.annotations["hmm_name"], "6CSM_D") self.assertEqual( alignment.target.annotations["hmm_description"], "GtACR1; rhodopsin, channelrhodopsin, anion channel, optogenetics; HET: RET, OLA; 2.9A {Guillardia theta CCMP2712}; Related PDB entries: 6CSM_B 6CSM_A 6CSM_C", ) self.assertEqual( alignment[0], "DGIKYVQL---VMAVVSACQVFFMVTRAPK------VPWEAIYLPTTEMITYSLAFTGNGYIRVA---NGKYLPWARMASWLCTCPIMLGLVSNMALVKYKSIPLNPMMIAASSICTVFGITASVVLDPLHVWLYCFISSIFFIFEMVVAFAIFAITIHDFQTIGSPMSLKVVERLKLMRIVFYVSWMAYPILWSFSSTGACIMSENTSSVLYLLGDALCKNTYGILLWATTWG", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHHHHHHHHTCSSCCTHHHHHHHHHHHHHHHHHTTCCEEEBTTSCEEEHHHHHHHHHHHHHHHHHHHTTCCCEETTEECHHHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHSTTTTCCSCHHHHHHHHHHHHCCCCCCHHHHHHCCCCC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHhCCCceecCCCccchHHHHHHHHHHHHHHHHHHHHHhcCCcccCChHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh ", ) self.assertEqual( str(alignment), """\ 6CSM_D 26 DGIKYVQL---VMAVVSACQVFFMVTRAPK------VPWEAIYLPTTEMITYSLAFTGNG 0 .......|---..........|........------........|......|.....|.| 4Y9H:A|PD 0 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG 6CSM_D 77 YIRVA---NGKYLPWARMASWLCTCPIMLGLVSNMALVKYKSIPLNPMMIAASSICTVFG 60 ...|.---......|||.|.||.|.|..|...........---........|..|....| 4Y9H:A|PD 60 LTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQ---GTILALVGADGIMIGTG 6CSM_D 134 ITASVVLDPLHVWLYCFISSIFFIFEMVVAFAIFAITIHDFQTIGSPMSLKVVERLKLMR 120 .................||.........|.|..-------|......|...|....|..| 4Y9H:A|PD 117 LVGALTKVYSYRFVWWAISTAAMLYILYVLFFG-------FTSKAESMRPEVASTFKVLR 6CSM_D 194 IVFYVSWMAYPILWSFSSTGACIMSENTSSVLYLLGDALCKNTYGILLWATTWG 248 180 .|..|.|.|||..|...|.||.|...|....|....|...|...|..|...... 234 4Y9H:A|PD 170 NVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 26, 34, 34, 53, 53, 82, 82, 114, 117, 167, 174, 248], [ 0, 8, 11, 30, 36, 65, 68, 100, 100, 150, 150, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['D', 'G', 'I', 'K', 'Y', 'V', 'Q', 'L', '-', '-', '-', 'V', 'M', 'A', 'V', 'V', 'S', 'A', 'C', 'Q', 'V', 'F', 'F', 'M', 'V', 'T', 'R', 'A', 'P', 'K', '-', '-', '-', '-', '-', '-', 'V', 'P', 'W', 'E', 'A', 'I', 'Y', 'L', 'P', 'T', 'T', 'E', 'M', 'I', 'T', 'Y', 'S', 'L', 'A', 'F', 'T', 'G', 'N', 'G', 'Y', 'I', 'R', 'V', 'A', '-', '-', '-', 'N', 'G', 'K', 'Y', 'L', 'P', 'W', 'A', 'R', 'M', 'A', 'S', 'W', 'L', 'C', 'T', 'C', 'P', 'I', 'M', 'L', 'G', 'L', 'V', 'S', 'N', 'M', 'A', 'L', 'V', 'K', 'Y', 'K', 'S', 'I', 'P', 'L', 'N', 'P', 'M', 'M', 'I', 'A', 'A', 'S', 'S', 'I', 'C', 'T', 'V', 'F', 'G', 'I', 'T', 'A', 'S', 'V', 'V', 'L', 'D', 'P', 'L', 'H', 'V', 'W', 'L', 'Y', 'C', 'F', 'I', 'S', 'S', 'I', 'F', 'F', 'I', 'F', 'E', 'M', 'V', 'V', 'A', 'F', 'A', 'I', 'F', 'A', 'I', 'T', 'I', 'H', 'D', 'F', 'Q', 'T', 'I', 'G', 'S', 'P', 'M', 'S', 'L', 'K', 'V', 'V', 'E', 'R', 'L', 'K', 'L', 'M', 'R', 'I', 'V', 'F', 'Y', 'V', 'S', 'W', 'M', 'A', 'Y', 'P', 'I', 'L', 'W', 'S', 'F', 'S', 'S', 'T', 'G', 'A', 'C', 'I', 'M', 'S', 'E', 'N', 'T', 'S', 'S', 'V', 'L', 'Y', 'L', 'L', 'G', 'D', 'A', 'L', 'C', 'K', 'N', 'T', 'Y', 'G', 'I', 'L', 'L', 'W', 'A', 'T', 'T', 'W', 'G'], ['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', '-', '-', '-', 'G', 'T', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', '-', '-', '-', '-', '-', '-', '-', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 5.8e-36, places=37) self.assertAlmostEqual(alignment.annotations["Score"], 247.02) self.assertAlmostEqual(alignment.annotations["Identities"], 24) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.317) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.900) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeeccCCCCCcchHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhh ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:224], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment[1], "GRPEWIWLALGTAL-MGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGT-----ILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIG-----SEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~~~~~~~v~~~RYv~W~ittPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~~~~~~~~s~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~g~~~lw~~~~i~~~~~~~~f~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~m~~~g~~~~~~RYi~W~~TtPlll~~l~~l~~~~~~~~~~~~~~~l~~~~~~mi~~G~~~~~~~~~~~~~~~~~~f~~~~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~~~~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~ll~~~~~ ", ) self.assertEqual(alignment.target.id, "6EYU_B") self.assertEqual( alignment.target.seq[8:226], "GGFGSQPFILAYIITAMISGLLFLYLPRKLDVPQKFGIIHFFIVVWSGLMYTNFLNQSFLSDYAWYMDWMVSTPLILLALGLTAFHGADTKRYDLLGALLGAEFTLVITGLLAQAQGSITPYYVGVLLLLGVVYLLAKPFREIAEESSDGLARAYKILAGYIGIFFLSYPTVWYISGIDALPGSLNILDPTQTSIALVVLPFFCKQVYGFLDMYLIHK", ) self.assertEqual(alignment.target.annotations["hmm_name"], "6EYU_B") self.assertEqual( alignment.target.annotations["hmm_description"], "Bacteriorhodopsin; Retinal protein, proton transport, MEMBRANE; HET: RET, LFA, MUN; 2.5A {Nanosalina sp. (strain J07AB43)}; Related PDB entries: 6EYU_C 6EYU_A", ) self.assertEqual( alignment[0], "GGFGSQPFILAYIITAMISGLLFLYLPRKL--DVPQKFGIIHFFIVVWSGLMYTNFLNQ-----------SFLSDYAWYMDWMVSTPLILLALGLTAFHGADTKRYDLLGALLGAEFTLVITGLLAQAQGS----ITPYYVGVLLLLGVVYLLAKPFREIAEESSDGLARAYKILAGYIGIFFLSYPTVWYISGIDALPGSLNILDPTQTSIALVVLPFFCKQVYGFLDMYLIHK", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHTTTTSCCTTGGGHHHHHHHHHHHHHHHHHHHHHHHTCSCCCHHHHHHHHHHHHHHHHHHHHHHHTTCSHHHHHHHHHHHHHHHHHHTHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHBCCSSSCSSCCCBCHHHHHHHHHHHHHCCCCCHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cccchHHHHHHHHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHchHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCcccCCHHHHHHHHHHHHHhhHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 6EYU_B 8 GGFGSQPFILAYIITAMISGLLFLYLPRKL--DVPQKFGIIHFFIVVWSGLMYTNFLNQ- 0 |........|....-.....|.||......--....||..|..........||...|..- 4Y9H:A|PD 0 GRPEWIWLALGTAL-MGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGY 6EYU_B 65 ----------SFLSDYAWYMDWMVSTPLILLALGLTAFHGADTKRYDLLGALLGAEFTLV 60 ----------......|.|.||...|||.||.|.|.......|-----..||.||..... 4Y9H:A|PD 59 GLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGT-----ILALVGADGIMI 6EYU_B 115 ITGLLAQAQGS----ITPYYVGVLLLLGVVYLLAKPFREIAEESSDGLARAYKILAGYIG 120 .|||.......----...........|...|.|...|...||......|...|.|..... 4Y9H:A|PD 114 GTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTV 6EYU_B 171 IFFLSYPTVWYISGIDALPGSLNILDPTQTSIALVVLPFFCKQVYGFLDMYLIHK 226 180 .....||.||.|.-----.....|...........||....|...|......... 235 4Y9H:A|PD 174 VLWSAYPVVWLIG-----SEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 224 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 8, 22, 23, 38, 38, 65, 65, 98, 103, 126, 126, 184, 189, 226], [ 0, 14, 14, 29, 31, 58, 69, 102, 102, 125, 129, 187, 187, 224]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'G', 'F', 'G', 'S', 'Q', 'P', 'F', 'I', 'L', 'A', 'Y', 'I', 'I', 'T', 'A', 'M', 'I', 'S', 'G', 'L', 'L', 'F', 'L', 'Y', 'L', 'P', 'R', 'K', 'L', '-', '-', 'D', 'V', 'P', 'Q', 'K', 'F', 'G', 'I', 'I', 'H', 'F', 'F', 'I', 'V', 'V', 'W', 'S', 'G', 'L', 'M', 'Y', 'T', 'N', 'F', 'L', 'N', 'Q', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'S', 'F', 'L', 'S', 'D', 'Y', 'A', 'W', 'Y', 'M', 'D', 'W', 'M', 'V', 'S', 'T', 'P', 'L', 'I', 'L', 'L', 'A', 'L', 'G', 'L', 'T', 'A', 'F', 'H', 'G', 'A', 'D', 'T', 'K', 'R', 'Y', 'D', 'L', 'L', 'G', 'A', 'L', 'L', 'G', 'A', 'E', 'F', 'T', 'L', 'V', 'I', 'T', 'G', 'L', 'L', 'A', 'Q', 'A', 'Q', 'G', 'S', '-', '-', '-', '-', 'I', 'T', 'P', 'Y', 'Y', 'V', 'G', 'V', 'L', 'L', 'L', 'L', 'G', 'V', 'V', 'Y', 'L', 'L', 'A', 'K', 'P', 'F', 'R', 'E', 'I', 'A', 'E', 'E', 'S', 'S', 'D', 'G', 'L', 'A', 'R', 'A', 'Y', 'K', 'I', 'L', 'A', 'G', 'Y', 'I', 'G', 'I', 'F', 'F', 'L', 'S', 'Y', 'P', 'T', 'V', 'W', 'Y', 'I', 'S', 'G', 'I', 'D', 'A', 'L', 'P', 'G', 'S', 'L', 'N', 'I', 'L', 'D', 'P', 'T', 'Q', 'T', 'S', 'I', 'A', 'L', 'V', 'V', 'L', 'P', 'F', 'F', 'C', 'K', 'Q', 'V', 'Y', 'G', 'F', 'L', 'D', 'M', 'Y', 'L', 'I', 'H', 'K'], ['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', '-', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F', 'G', 'G', 'E', 'Q', 'N', 'P', 'I', 'Y', 'W', 'A', 'R', 'Y', 'A', 'D', 'W', 'L', 'F', 'T', 'T', 'P', 'L', 'L', 'L', 'L', 'D', 'L', 'A', 'L', 'L', 'V', 'D', 'A', 'D', 'Q', 'G', 'T', '-', '-', '-', '-', '-', 'I', 'L', 'A', 'L', 'V', 'G', 'A', 'D', 'G', 'I', 'M', 'I', 'G', 'T', 'G', 'L', 'V', 'G', 'A', 'L', 'T', 'K', 'V', 'Y', 'S', 'Y', 'R', 'F', 'V', 'W', 'W', 'A', 'I', 'S', 'T', 'A', 'A', 'M', 'L', 'Y', 'I', 'L', 'Y', 'V', 'L', 'F', 'F', 'G', 'F', 'T', 'S', 'K', 'A', 'E', 'S', 'M', 'R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', '-', '-', '-', '-', '-', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 99.28) self.assertAlmostEqual(alignment.annotations["E-value"], 1.4e-15, places=16) self.assertAlmostEqual(alignment.annotations["Score"], 102.00) self.assertAlmostEqual(alignment.annotations["Identities"], 100) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.503) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.200) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhhC", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[158:226], "RPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment[1], "RPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~~~l~~~~~i~W~~YPi~w~l~~~g~~~i~~~~~~~~~~ilDi~~K~~f~~~l~~~~~~~~", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~~~~l~~~~~v~W~~YPi~w~lg~~g~~~i~~~~~~i~y~ilDv~~K~~fg~~~l~~~~~~~", ) self.assertEqual(alignment.target.id, "1BCT_A") self.assertEqual( alignment.target.seq[1:69], "RPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1BCT_A") self.assertEqual( alignment.target.annotations["hmm_description"], "BACTERIORHODOPSIN (FRAGMENT 163-231) (NMR, 14; PHOTORECEPTOR; NMR {Halobacterium salinarum} SCOP: j.35.1.1", ) self.assertEqual( alignment[0], "RPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCCHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC", ) self.assertEqual( str(alignment), """\ 1BCT_A 1 RPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLIL 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 4Y9H:A|PD 158 RPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLIL 1BCT_A 61 LRSRAIFG 69 60 |||||||| 68 4Y9H:A|PD 218 LRSRAIFG 226 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 1, 69], [158, 226]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F', 'G'], ['R', 'P', 'E', 'V', 'A', 'S', 'T', 'F', 'K', 'V', 'L', 'R', 'N', 'V', 'T', 'V', 'V', 'L', 'W', 'S', 'A', 'Y', 'P', 'V', 'V', 'W', 'L', 'I', 'G', 'S', 'E', 'G', 'A', 'G', 'I', 'V', 'P', 'L', 'N', 'I', 'E', 'T', 'L', 'L', 'F', 'M', 'V', 'L', 'D', 'V', 'S', 'A', 'K', 'V', 'G', 'F', 'G', 'L', 'I', 'L', 'L', 'R', 'S', 'R', 'A', 'I', 'F', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 98.44) self.assertAlmostEqual(alignment.annotations["E-value"], 2e-10, places=10) self.assertAlmostEqual(alignment.annotations["Score"], 77.33) self.assertAlmostEqual(alignment.annotations["Identities"], 97) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.598) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.100) self.assertEqual( alignment.query.letter_annotations["ss_pred"], "CCcHHHHHHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCCCceeecc ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[0:66], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPF", ) self.assertEqual( alignment[1], "GRPEWIWLALGTALMGLGTLYFLVKGMG-VSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPF", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], "~~~~~~~~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~g~~~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~lw~~~~~m~~~~~~f~~~s~~~~~~~~R~~~~~~~~i~~iaaiaY~~MA~g~G~~~v~~", ) self.assertEqual(alignment.target.id, "1BHA_A") self.assertEqual( alignment.target.seq[5:71], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPF", ) self.assertEqual(alignment.target.annotations["hmm_name"], "1BHA_A") self.assertEqual( alignment.target.annotations["hmm_description"], "BACTERIORHODOPSIN (PROTEOLYTIC FRAGMENT 1 -; PHOTORECEPTOR; NMR {Halobacterium salinarum} SCOP: j.35.1.1; Related PDB entries: 1BHB_A", ) self.assertEqual( alignment[0], "GRPEWIWLALGTALMGLGTLYFLVKGMGVSD-PDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPF", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " SCHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHSHHHHHHHHHHHHHTCSSSSCC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ChhHHHHHHHHHHHHHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHHHHHHHHHHHhcCCcccCCC", ) self.assertEqual( str(alignment), """\ 1BHA_A 5 GRPEWIWLALGTALMGLGTLYFLVKGMGVSD-PDAKKFYAITTLVPAIAFTMYLSMLLGY 0 ||||||||||||||||||||||||||||-..-|||||||||||||||||||||||||||| 4Y9H:A|PD 0 GRPEWIWLALGTALMGLGTLYFLVKGMG-VSDPDAKKFYAITTLVPAIAFTMYLSMLLGY 1BHA_A 64 GLTMVPF 71 60 ||||||| 67 4Y9H:A|PD 59 GLTMVPF 66 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 5, 33, 34, 36, 36, 71], [ 0, 28, 28, 30, 31, 66]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', '-', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F'], ['G', 'R', 'P', 'E', 'W', 'I', 'W', 'L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', '-', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y', 'G', 'L', 'T', 'M', 'V', 'P', 'F']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 96.55) self.assertAlmostEqual(alignment.annotations["E-value"], 3.3e-05) self.assertAlmostEqual(alignment.annotations["Score"], 51.24) self.assertAlmostEqual(alignment.annotations["Identities"], 31) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.326) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 4.800) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHhCC ", ) self.assertEqual(alignment.query.id, "4Y9H:A|PDBID|CHAIN|SEQUENCE") self.assertEqual( alignment.query.seq[7:59], "LALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGY", ) self.assertEqual( alignment[1], "LALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGY" ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~m~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " fs~g~aaM~AatvfF~l~~~~V~~~yr~s~~lsalVt~iA~~hY~~m~~~W ", ) self.assertEqual(alignment.target.id, "5ABB_Z") self.assertEqual( alignment.target.seq[14:65], "FWLVTAALLASTVFFFVERDRVSAKWKTSLTVSGLVTGIAFWHYMYMRGVW", ) self.assertEqual(alignment.target.annotations["hmm_name"], "5ABB_Z") self.assertEqual( alignment.target.annotations["hmm_description"], "PROTEIN TRANSLOCASE SUBUNIT SECY, PROTEIN; TRANSLATION, RIBOSOME, MEMBRANE PROTEIN, TRANSLOCON; 8.0A {ESCHERICHIA COLI}", ) self.assertEqual( alignment[0], "FWLVTAALLASTVFFFVERDRVS-AKWKTSLTVSGLVTGIAFWHYMYMRGVW" ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " HHHHHHHHHHHHHHHHTTTSSCCSCCCCSSSCHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HHHHHHHHHHHHHHHHHHhhccChhhhHHHHHHHHHHHHHHHHHHHHHHHH ", ) self.assertEqual( str(alignment), """\ 5ABB_Z 14 FWLVTAALLASTVFFFVERDRVS-AKWKTSLTVSGLVTGIAFWHYMYMRGVW 65 0 ..|.||.....|..|.|....||-...|.......||..|||..|..|.... 52 4Y9H:A|PD 7 LALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGY 59 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14, 37, 37, 65], [ 7, 30, 31, 59]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['F', 'W', 'L', 'V', 'T', 'A', 'A', 'L', 'L', 'A', 'S', 'T', 'V', 'F', 'F', 'F', 'V', 'E', 'R', 'D', 'R', 'V', 'S', '-', 'A', 'K', 'W', 'K', 'T', 'S', 'L', 'T', 'V', 'S', 'G', 'L', 'V', 'T', 'G', 'I', 'A', 'F', 'W', 'H', 'Y', 'M', 'Y', 'M', 'R', 'G', 'V', 'W'], ['L', 'A', 'L', 'G', 'T', 'A', 'L', 'M', 'G', 'L', 'G', 'T', 'L', 'Y', 'F', 'L', 'V', 'K', 'G', 'M', 'G', 'V', 'S', 'D', 'P', 'D', 'A', 'K', 'K', 'F', 'Y', 'A', 'I', 'T', 'T', 'L', 'V', 'P', 'A', 'I', 'A', 'F', 'T', 'M', 'Y', 'L', 'S', 'M', 'L', 'L', 'G', 'Y']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_length(self): """Test getting the number of alignments without parsing the file.""" stream = open(self.path) alignments = Align.parse(stream, "hhr") stream.close() self.assertEqual(len(alignments), 29) class Align_hhr_hhpred_9590198(unittest.TestCase): path = os.path.join("HHsuite", "hhpred_9590198.hhr") def test_reading(self): alignments = Align.parse(self.path, "hhr") self.assertEqual(alignments.metadata["No_of_seqs"], (157, 584)) self.assertAlmostEqual(alignments.metadata["Neff"], 6.82639) self.assertEqual(alignments.metadata["Searched_HMMs"], 64707) self.assertEqual(alignments.metadata["Rundate"], "Fri Feb 1 15:48:30 2019") self.assertEqual( alignments.metadata["Command line"], "hhsearch -cpu 8 -i ../results/full.a3m -d /cluster/toolkit/production/databases/hh-suite/mmcif70/pdb70 -d /cluster/toolkit/production/databases/hh-suite/pfama/pfama -o ../results/9590198.hhr -oa3m ../results/9590198.a3m -p 20 -Z 250 -loc -z 1 -b 1 -B 250 -ssm 2 -sc 1 -seq 1 -dbstrlen 10000 -norealign -maxres 32000 -contxt /cluster/toolkit/production/bioprogs/tools/hh-suite-build/data/context_data.crf", ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 9.9e-102, places=103) self.assertAlmostEqual(alignment.annotations["Score"], 792.76) self.assertAlmostEqual(alignment.annotations["Identities"], 53) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.957) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.100) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CCcHHHHHHHHHHccCCcCcEEEEECCCCCcCCCEEEEeCCCCeEEEecCccceeeEEEEecCCCCEEEECCEEecCCCCCCcHHHHHHhhcCCCCCCccCcccEEEEEeCcEEEEeeCcccCCCCccCCCcccccccCCCCCCCeEEEEEEEeCCChHhcCCCCCCcccccCcceeeEEEEeeCCCCCceEEEEEEecCCCCccccccceeEEEEEEEecCCHHHHHHHhcCCcEEEEeccccccccCCCCCcCCCCcCCccchhhHhhccceeecCCCCEEEEEEecCCCCCCccccccccCcEEeeccccccCCCCCcceeccCcCHHHHHHHhCCCCCCCeEeeCCCCCCCCCCCCceEEeccCCEEEEEecCCCEEEEEEe ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[21:407], "GMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKRMYIYSGNSLQDTKAPMMPLSCFLGNVYAESVDVLRDGTGPAGLRLRLLAAGCGPGLLADAKMRVFERSVYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTNYPGHYNFNIYHRCEFKIPLAIKKENADGQTETCTTYSKWDNIQELLGHPVEKPVVLHRSSSPNNTNPFGSTFCFGLQRMIFEVMQNNHIASVTLY", ) self.assertEqual( alignment[1], "GMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGA--TVKRMYIYSGNSLQ---------DTKA-PMMPLSCFLGNVYAESVDVLRDGTGPAGLRLRLLAAGCGPGLLADAKMRVFERSVYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTNYPGHYNFNIYHRCEFKIPLAIKKENADG------QTETCTTYSKWDNIQELLGHPVEKPVVLHRSSSPNNTNPFGSTFCFGLQRMIFEVMQNNHIASVTLY", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " G~sL~~vi~~Lr~~~~~~~~vel~Ys~~~pl~~~Ivi~L~~~GirL~Fd~~~QrL~lIEv~d~~~~~L~Y~~~~~~~~~~~ptf~~I~~~FGPTyPG~yd~~~~~Y~LsYpGisF~Fpi~~~~~~~~~~~~~~~~l~~l~~~~~~~~s~i~If~G~s~~~~~~~~~p~~~~~~~~~~~~v~v~~~~~~~~gl~~~~~~~~~~~~~~~~~~~~~~~~~I~~G~T~QDVl~~LG~P~~~f~K~ddrm~IH~~~~~~~~~~~~~dyF~NYF~lG~DiLfd~~t~~v~KiILHtN~PG~~~F~~Y~RC~w~i~~~~~~~~~~~~~~~it~~~~~~~i~~~l~~~~~~pvvlnR~~s~~~~~~fg~T~~yG~~g~IfEVm~ng~IasvTl~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "G~~L~~vi~~L~~~~~~~~~Vel~Ys~~~p~~~~Ivl~L~~~glrL~Fd~~~QrL~lIEv~d~~~~~L~Y~~~~~~~~~~~~t~~~Iy~~FGPTyPG~~d~~~~~y~LsYpGisF~F~~~~~~~~~~~~~~~~l~~~~~~~~~~~~m~If~G~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~~~~v~v~~~~~~~~gl~l~f~~~~~~~~~~~~~~~~~~~I~~G~t~QDVl~~LG~P~~~f~K~ddrm~Ih~~~~~~~~~~~~~yF~NYF~lG~DiLfd~~th~v~KiILHtN~Pg~~~F~~Y~RC~~~l~~~~~~~~~~~~~~~~~~~~i~~~~~~~~i~~~l~~~~~p~vlnR~~~~~~~~~~g~T~lyg~~g~ifEV~~ng~Iasvtlf", ) self.assertEqual(alignment.target.id, "H9J4A9_BOMMO/5") self.assertEqual( alignment.target.seq[0:394], "GMHFSQSVAIIQSQVGTIRGVQVLYSDQNPLSVDLVINMPQDGMRLIFDPVAQRLKIIEIYNMKLVKLRYSGMCFNSPEITPSIEQVEHCFGATHPGLYDSQRHLFALNFRGLSFYFPVDSKFEPGYAHGLGSLQFPNGGSPVVSRTTIYYGSQHQLSSNTSSRVSGVPLPDLPLSCYRQQLHLRRCDVLRNTTSTMGLRLHMFTEGTSRALEPSQVALVRVVRFGDSCQGVARALGAPARLYYKADDKMRIHRPTARRRPPPASDYLFNYFTLGLDVLFDARTNQVKKFVLHTNYPGHYNFNMYHRCEFELTVQPDKSEAHSLVESGGGVAVTAYSKWEVVSRALRVCERPVVLNRASSTNTTNPFGSTFCYGYQDIIFEVMSNNYIASITLY", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF03676.14") self.assertEqual( alignment.target.annotations["hmm_description"], "; UPF0183 ; Uncharacterised protein family (UPF0183)", ) self.assertEqual( alignment[0], "GMHFSQSVAIIQSQVGTIRGVQVLYSDQNPLSVDLVINMPQDGMRLIFDPVAQRLKIIEIYNMKLVKLRYSGMCFNSPEITPSIEQVEHCFGATHPGLYDSQRHLFALNFRGLSFYFPVDS-----KFEPGYAHGLGSLQFPNGGSPVVSRTTIYYGSQHQLSSNTSSRVSGVPLPDLPLSCYRQQLHLRRCDVLRNTTSTMGLRLHMFTEGT--SRALEPSQVALVRVVRFGDSCQGVARALGAPARLYYKADDKMRIHRPTARRR-PPPASDYLFNYFTLGLDVLFDARTNQVKKFVLHTNYPGHYNFNMYHRCEFELTVQPD-KSEAHSLVESGGGVAVTAYSKWEVVSRAL-RVCERPVVLNRASSTNTTNPFGSTFCYGYQDIIFEVMSNNYIASITLY", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCcHHHHHHHHHhcCCccceEEEEECCCCCCCCcEEEEcCCCceEEEEcCccCeEEEEEEEcCCCcEEEEcCeeecCCCCCCcHHHHHHHhcCCCCCcccCCCCeEEEEeCcEEEEeeCCcccCCCCccccccccCCCCCCCceEEEEEEeCCccccccccccccCCCCCCCCCchhcCCCCceEEEEEEEcCCCCceEEEEEEcCCCCCcCCccceeceEEEEecCCHHHHHHHhCCCceEEEcCcccccccCCCCCCCCCCcchhchhHHHhCcceeecCCCcEEEEEEeeCCCCCCccccccccCeEEEEeCCCcchhcceecCCCCceecCcccHHHHHHHhccCCCCEEEecCCCCCCCCCCCcEEEEecCCEEEEEecCCcEEEEEeC", ) self.assertEqual( str(alignment), """\ H9J4A9_BO 0 GMHFSQSVAIIQSQVGTIRGVQVLYSDQNPLSVDLVINMPQDGMRLIFDPVAQRLKIIEI 0 ||...|.|||.|.....|..||||||.|.|||.||..|..|||..|.||...||||.||. sp|Q9BSU1 21 GMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEV H9J4A9_BO 60 YNMKLVKLRYSGMCFNSPEITPSIEQVEHCFGATHPGLYDSQRHLFALNFRGLSFYFPVD 60 .....|||.|.|..|||..|.|.|||....|||||||.|.|...||.||||||||.|..| sp|Q9BSU1 81 CDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQLD H9J4A9_BO 120 S-----KFEPGYAHGLGSLQFPNGGSPVVSRTTIYYGSQHQLSSNTSSRVSGVPLPDLPL 120 |-----|.||..||||.|||.|.|.--.|.|..||.|...|---------....-|..|| sp|Q9BSU1 141 SWTEAPKYEPNFAHGLASLQIPHGA--TVKRMYIYSGNSLQ---------DTKA-PMMPL H9J4A9_BO 175 SCYRQQLHLRRCDVLRNTTSTMGLRLHMFTEGT--SRALEPSQVALVRVVRFGDSCQGVA 180 ||..........||||..|...||||.....|.--............|.|.||||||.|. sp|Q9BSU1 189 SCFLGNVYAESVDVLRDGTGPAGLRLRLLAAGCGPGLLADAKMRVFERSVYFGDSCQDVL H9J4A9_BO 233 RALGAPARLYYKADDKMRIHRPTARRR-PPPASDYLFNYFTLGLDVLFDARTNQVKKFVL 240 ..||.|....||..|||.||.|.....-|....||.|||||||.|.||||.|..|||||| sp|Q9BSU1 249 SMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVL H9J4A9_BO 292 HTNYPGHYNFNMYHRCEFELTVQPD-KSEAHSLVESGGGVAVTAYSKWEVVSRAL-RVCE 300 |||||||||||.||||||.......-.....------.....|.||||......|-...| sp|Q9BSU1 309 HTNYPGHYNFNIYHRCEFKIPLAIKKENADG------QTETCTTYSKWDNIQELLGHPVE H9J4A9_BO 350 RPVVLNRASSTNTTNPFGSTFCYGYQDIIFEVMSNNYIASITLY 394 360 .||||.|.||.|.|||||||||.|.|..|||||.||.|||.||| 404 sp|Q9BSU1 363 KPVVLHRSSSPNNTNPFGSTFCFGLQRMIFEVMQNNHIASVTLY 407 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 121, 121, 140, 142, 156, 165, 169, 170, 208, 208, 260, 260, 317, 317, 322, 328, 346, 346, 394], [ 21, 142, 147, 166, 166, 180, 180, 184, 184, 222, 224, 276, 277, 334, 335, 340, 340, 358, 359, 407]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'M', 'H', 'F', 'S', 'Q', 'S', 'V', 'A', 'I', 'I', 'Q', 'S', 'Q', 'V', 'G', 'T', 'I', 'R', 'G', 'V', 'Q', 'V', 'L', 'Y', 'S', 'D', 'Q', 'N', 'P', 'L', 'S', 'V', 'D', 'L', 'V', 'I', 'N', 'M', 'P', 'Q', 'D', 'G', 'M', 'R', 'L', 'I', 'F', 'D', 'P', 'V', 'A', 'Q', 'R', 'L', 'K', 'I', 'I', 'E', 'I', 'Y', 'N', 'M', 'K', 'L', 'V', 'K', 'L', 'R', 'Y', 'S', 'G', 'M', 'C', 'F', 'N', 'S', 'P', 'E', 'I', 'T', 'P', 'S', 'I', 'E', 'Q', 'V', 'E', 'H', 'C', 'F', 'G', 'A', 'T', 'H', 'P', 'G', 'L', 'Y', 'D', 'S', 'Q', 'R', 'H', 'L', 'F', 'A', 'L', 'N', 'F', 'R', 'G', 'L', 'S', 'F', 'Y', 'F', 'P', 'V', 'D', 'S', '-', '-', '-', '-', '-', 'K', 'F', 'E', 'P', 'G', 'Y', 'A', 'H', 'G', 'L', 'G', 'S', 'L', 'Q', 'F', 'P', 'N', 'G', 'G', 'S', 'P', 'V', 'V', 'S', 'R', 'T', 'T', 'I', 'Y', 'Y', 'G', 'S', 'Q', 'H', 'Q', 'L', 'S', 'S', 'N', 'T', 'S', 'S', 'R', 'V', 'S', 'G', 'V', 'P', 'L', 'P', 'D', 'L', 'P', 'L', 'S', 'C', 'Y', 'R', 'Q', 'Q', 'L', 'H', 'L', 'R', 'R', 'C', 'D', 'V', 'L', 'R', 'N', 'T', 'T', 'S', 'T', 'M', 'G', 'L', 'R', 'L', 'H', 'M', 'F', 'T', 'E', 'G', 'T', '-', '-', 'S', 'R', 'A', 'L', 'E', 'P', 'S', 'Q', 'V', 'A', 'L', 'V', 'R', 'V', 'V', 'R', 'F', 'G', 'D', 'S', 'C', 'Q', 'G', 'V', 'A', 'R', 'A', 'L', 'G', 'A', 'P', 'A', 'R', 'L', 'Y', 'Y', 'K', 'A', 'D', 'D', 'K', 'M', 'R', 'I', 'H', 'R', 'P', 'T', 'A', 'R', 'R', 'R', '-', 'P', 'P', 'P', 'A', 'S', 'D', 'Y', 'L', 'F', 'N', 'Y', 'F', 'T', 'L', 'G', 'L', 'D', 'V', 'L', 'F', 'D', 'A', 'R', 'T', 'N', 'Q', 'V', 'K', 'K', 'F', 'V', 'L', 'H', 'T', 'N', 'Y', 'P', 'G', 'H', 'Y', 'N', 'F', 'N', 'M', 'Y', 'H', 'R', 'C', 'E', 'F', 'E', 'L', 'T', 'V', 'Q', 'P', 'D', '-', 'K', 'S', 'E', 'A', 'H', 'S', 'L', 'V', 'E', 'S', 'G', 'G', 'G', 'V', 'A', 'V', 'T', 'A', 'Y', 'S', 'K', 'W', 'E', 'V', 'V', 'S', 'R', 'A', 'L', '-', 'R', 'V', 'C', 'E', 'R', 'P', 'V', 'V', 'L', 'N', 'R', 'A', 'S', 'S', 'T', 'N', 'T', 'T', 'N', 'P', 'F', 'G', 'S', 'T', 'F', 'C', 'Y', 'G', 'Y', 'Q', 'D', 'I', 'I', 'F', 'E', 'V', 'M', 'S', 'N', 'N', 'Y', 'I', 'A', 'S', 'I', 'T', 'L', 'Y'], ['G', 'M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'C', 'D', 'L', 'T', 'K', 'V', 'K', 'L', 'K', 'Y', 'C', 'G', 'V', 'H', 'F', 'N', 'S', 'Q', 'A', 'I', 'A', 'P', 'T', 'I', 'E', 'Q', 'I', 'D', 'Q', 'S', 'F', 'G', 'A', 'T', 'H', 'P', 'G', 'V', 'Y', 'N', 'S', 'A', 'E', 'Q', 'L', 'F', 'H', 'L', 'N', 'F', 'R', 'G', 'L', 'S', 'F', 'S', 'F', 'Q', 'L', 'D', 'S', 'W', 'T', 'E', 'A', 'P', 'K', 'Y', 'E', 'P', 'N', 'F', 'A', 'H', 'G', 'L', 'A', 'S', 'L', 'Q', 'I', 'P', 'H', 'G', 'A', '-', '-', 'T', 'V', 'K', 'R', 'M', 'Y', 'I', 'Y', 'S', 'G', 'N', 'S', 'L', 'Q', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'D', 'T', 'K', 'A', '-', 'P', 'M', 'M', 'P', 'L', 'S', 'C', 'F', 'L', 'G', 'N', 'V', 'Y', 'A', 'E', 'S', 'V', 'D', 'V', 'L', 'R', 'D', 'G', 'T', 'G', 'P', 'A', 'G', 'L', 'R', 'L', 'R', 'L', 'L', 'A', 'A', 'G', 'C', 'G', 'P', 'G', 'L', 'L', 'A', 'D', 'A', 'K', 'M', 'R', 'V', 'F', 'E', 'R', 'S', 'V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F', 'Y', 'K', 'S', 'E', 'D', 'K', 'M', 'K', 'I', 'H', 'S', 'P', 'S', 'P', 'H', 'K', 'Q', 'V', 'P', 'S', 'K', 'C', 'N', 'D', 'Y', 'F', 'F', 'N', 'Y', 'F', 'T', 'L', 'G', 'V', 'D', 'I', 'L', 'F', 'D', 'A', 'N', 'T', 'H', 'K', 'V', 'K', 'K', 'F', 'V', 'L', 'H', 'T', 'N', 'Y', 'P', 'G', 'H', 'Y', 'N', 'F', 'N', 'I', 'Y', 'H', 'R', 'C', 'E', 'F', 'K', 'I', 'P', 'L', 'A', 'I', 'K', 'K', 'E', 'N', 'A', 'D', 'G', '-', '-', '-', '-', '-', '-', 'Q', 'T', 'E', 'T', 'C', 'T', 'T', 'Y', 'S', 'K', 'W', 'D', 'N', 'I', 'Q', 'E', 'L', 'L', 'G', 'H', 'P', 'V', 'E', 'K', 'P', 'V', 'V', 'L', 'H', 'R', 'S', 'S', 'S', 'P', 'N', 'N', 'T', 'N', 'P', 'F', 'G', 'S', 'T', 'F', 'C', 'F', 'G', 'L', 'Q', 'R', 'M', 'I', 'F', 'E', 'V', 'M', 'Q', 'N', 'N', 'H', 'I', 'A', 'S', 'V', 'T', 'L', 'Y']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 71.77) self.assertAlmostEqual(alignment.annotations["E-value"], 67) self.assertAlmostEqual(alignment.annotations["Score"], 28.65) self.assertAlmostEqual(alignment.annotations["Identities"], 14) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.172) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEEEEeccccccccCCCCCcCCCCcCCccchhhHhhccceeecCCCCEEEEEEecCCCCCCccccccccCcEEeeccccccCCCCCcceeccCcCHHHHHHHhCCCCCCCeEeeCCCCCCCCCCCCceEEeccCCEEEEEecCCCEEEEEEeCC ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[238:409], "VYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTNYPGHYNFNIYHRCEFKIPLAIKKENADGQTETCTTYSKWDNIQELLGHPVEKPVVLHRSSSPNNTNPFGSTFCFGLQRMIFEVMQNNHIASVTLYGP", ) self.assertEqual( alignment[1], "VYF---------GDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVL-----HTNYPGHYNFNIYHRCEFKIPLAIKKENADGQTETCTTYSKWDNIQELLGHPVEKPVVLHRSSSPNNTNPFGSTFCFGLQ------RMIFEVM-QNNHIASVTLYGP", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~f~K~ddrm~IH~~~~~~~~~~~~~dyF~NYF~lG~DiLfd~~t~~v~KiILHtN~PG~~~F~~Y~RC~w~i~~~~~~~~~~~~~~~it~~~~~~~i~~~l~~~~~~pvvlnR~~s~~~~~~fg~T~~yG~~g~IfEVm~ng~IasvTl~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~~~~~~~~~~~G~t~~eV~~~lG~p~~~~~~~~~~~~~~~~~w~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~i~~G~t~~eV~~~lG~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~F~~g~l~~~~~~g~", ) self.assertEqual(alignment.target.id, "Q8DTX1_STRMU/4") self.assertEqual( alignment.target.seq[11:159], "IKVTTDQNHFSGGTSIEQLKQWFGDPNKSEQRNAGNITLDSYTWVKDGAVINAQLYKNSTVARSISNFSFSREAKIGKEDYDELKIGESYKKVVEKLGEPDVLSQSMSSDKEEMQTVWSSGIKTKSSSATIELYFENGLLKNKTQKDL", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF12978.7") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF3862 ; Domain of Unknown Function with PDB structure (DUF3862)", ) self.assertEqual( alignment[0], "IKVTTDQNHFSGGTSIEQLKQWFGDPNKSEQRNAG-------------NITLDSYTWVKDGAVINAQLY-KNSTVARSISNFSFSREAKIGKEDYD-----------------------ELKIGESYKKVVEKL----GEPDVLSQSMS---SDKEEMQTVWSSGIKTKSSSATIELYFENGLLKNKTQKDL", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " eeecCCcccCCCCCCHHHHHHHHCCCceEEeeeeCCeEEEEEEEEeCCeEEEEEEECCEEEEEEEEeceecCCCCCCHHHHHhcCCCCCHHHHHHHHCCCCeeEEEeeCCceEEEEEEEecccCCCCCcEEEEEEECCeEEEeEecCC", ) self.assertEqual( str(alignment), """\ Q8DTX1_ST 11 IKVTTDQNHFSGGTSIEQLKQWFGDPNKSEQRNAG-------------NITLDSYTWVKD 0 ...---------|.|........|.|.|.......-------------......|..... sp|Q9BSU1 238 VYF---------GDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYF Q8DTX1_ST 58 GAVINAQLY-KNSTVARSISNFSFSREAKIGKEDYD-----------------------E 60 .........-....|.....-----.....|.....-----------------------. sp|Q9BSU1 289 TLGVDILFDANTHKVKKFVL-----HTNYPGHYNFNIYHRCEFKIPLAIKKENADGQTET Q8DTX1_ST 94 LKIGESYKKVVEKL----GEPDVLSQSMS---SDKEEMQTVWSSGIKTKSSSATIELYFE 120 ...........|.|----..|.||..|.|---.............------....|..-. sp|Q9BSU1 344 CTTYSKWDNIQELLGHPVEKPVVLHRSSSPNNTNPFGSTFCFGLQ------RMIFEVM-Q Q8DTX1_ST 147 NGLLKNKTQKDL 159 180 |......|.... 192 sp|Q9BSU1 397 NNHIASVTLYGP 409 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 11, 14, 23, 46, 46, 67, 67, 77, 82, 93, 93, 108, 108, 119, 119, 132, 138, 145, 146, 159], [238, 241, 241, 264, 277, 298, 299, 309, 309, 320, 343, 358, 362, 373, 376, 389, 389, 396, 396, 409]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'K', 'V', 'T', 'T', 'D', 'Q', 'N', 'H', 'F', 'S', 'G', 'G', 'T', 'S', 'I', 'E', 'Q', 'L', 'K', 'Q', 'W', 'F', 'G', 'D', 'P', 'N', 'K', 'S', 'E', 'Q', 'R', 'N', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'N', 'I', 'T', 'L', 'D', 'S', 'Y', 'T', 'W', 'V', 'K', 'D', 'G', 'A', 'V', 'I', 'N', 'A', 'Q', 'L', 'Y', '-', 'K', 'N', 'S', 'T', 'V', 'A', 'R', 'S', 'I', 'S', 'N', 'F', 'S', 'F', 'S', 'R', 'E', 'A', 'K', 'I', 'G', 'K', 'E', 'D', 'Y', 'D', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'E', 'L', 'K', 'I', 'G', 'E', 'S', 'Y', 'K', 'K', 'V', 'V', 'E', 'K', 'L', '-', '-', '-', '-', 'G', 'E', 'P', 'D', 'V', 'L', 'S', 'Q', 'S', 'M', 'S', '-', '-', '-', 'S', 'D', 'K', 'E', 'E', 'M', 'Q', 'T', 'V', 'W', 'S', 'S', 'G', 'I', 'K', 'T', 'K', 'S', 'S', 'S', 'A', 'T', 'I', 'E', 'L', 'Y', 'F', 'E', 'N', 'G', 'L', 'L', 'K', 'N', 'K', 'T', 'Q', 'K', 'D', 'L'], ['V', 'Y', 'F', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F', 'Y', 'K', 'S', 'E', 'D', 'K', 'M', 'K', 'I', 'H', 'S', 'P', 'S', 'P', 'H', 'K', 'Q', 'V', 'P', 'S', 'K', 'C', 'N', 'D', 'Y', 'F', 'F', 'N', 'Y', 'F', 'T', 'L', 'G', 'V', 'D', 'I', 'L', 'F', 'D', 'A', 'N', 'T', 'H', 'K', 'V', 'K', 'K', 'F', 'V', 'L', '-', '-', '-', '-', '-', 'H', 'T', 'N', 'Y', 'P', 'G', 'H', 'Y', 'N', 'F', 'N', 'I', 'Y', 'H', 'R', 'C', 'E', 'F', 'K', 'I', 'P', 'L', 'A', 'I', 'K', 'K', 'E', 'N', 'A', 'D', 'G', 'Q', 'T', 'E', 'T', 'C', 'T', 'T', 'Y', 'S', 'K', 'W', 'D', 'N', 'I', 'Q', 'E', 'L', 'L', 'G', 'H', 'P', 'V', 'E', 'K', 'P', 'V', 'V', 'L', 'H', 'R', 'S', 'S', 'S', 'P', 'N', 'N', 'T', 'N', 'P', 'F', 'G', 'S', 'T', 'F', 'C', 'F', 'G', 'L', 'Q', '-', '-', '-', '-', '-', '-', 'R', 'M', 'I', 'F', 'E', 'V', 'M', '-', 'Q', 'N', 'N', 'H', 'I', 'A', 'S', 'V', 'T', 'L', 'Y', 'G', 'P']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 70.25) self.assertAlmostEqual(alignment.annotations["E-value"], 4.9) self.assertAlmostEqual(alignment.annotations["Score"], 30.39) self.assertAlmostEqual(alignment.annotations["Identities"], 30) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.363) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 10.200) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~~Gmt~~eV~~~lG~P~~~ ", ) self.assertEqual(alignment.target.id, "A6W2D6_MARMS/3") self.assertEqual(alignment.target.seq[11:31], "LQIGMSESQVTYLLGNPMLR") self.assertEqual(alignment.target.annotations["hmm_name"], "PF04355.13") self.assertEqual( alignment.target.annotations["hmm_description"], "; SmpA_OmlA ; SmpA / OmlA family", ) self.assertEqual(alignment[0], "LQIGMSESQVTYLLGNPMLR") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHHCCCcee ", ) self.assertEqual( str(alignment), """\ A6W2D6_MA 11 LQIGMSESQVTYLLGNPMLR 31 0 ...|.|...|...||.|... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 11, 31], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'Q', 'I', 'G', 'M', 'S', 'E', 'S', 'Q', 'V', 'T', 'Y', 'L', 'L', 'G', 'N', 'P', 'M', 'L', 'R'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 68.06) self.assertAlmostEqual(alignment.annotations["E-value"], 5.9) self.assertAlmostEqual(alignment.annotations["Score"], 32.02) self.assertAlmostEqual(alignment.annotations["Identities"], 30) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.380) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " l~~G~t~~eV~~~lG~P~~~ ", ) self.assertEqual(alignment.target.id, "5EKQ_E") self.assertEqual(alignment.target.seq[26:46], "IRVGMTQQQVAYALGTPLMS") self.assertEqual(alignment.target.annotations["hmm_name"], "5EKQ_E") self.assertEqual( alignment.target.annotations["hmm_description"], "Outer membrane protein assembly factor; membrane protein, insertase, beta-barrel, outer; 3.392A {Escherichia coli (strain K12)}; Related PDB entries: 2KM7_A 2KXX_A 5AYW_E 5LJO_E", ) self.assertEqual(alignment[0], "IRVGMTQQQVAYALGTPLMS") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCTTCCSTTTTTSSCCCSEE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHhCCCcee ", ) self.assertEqual( str(alignment), """\ 5EKQ_E 26 IRVGMTQQQVAYALGTPLMS 46 0 ...|...|.|...||.|... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 26, 46], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'R', 'V', 'G', 'M', 'T', 'Q', 'Q', 'Q', 'V', 'A', 'Y', 'A', 'L', 'G', 'T', 'P', 'L', 'M', 'S'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 58.72) self.assertAlmostEqual(alignment.annotations["E-value"], 13) self.assertAlmostEqual(alignment.annotations["Score"], 30.74) self.assertAlmostEqual(alignment.annotations["Identities"], 15) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.388) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.500) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~~Gmtk~eV~~~lG~P~~~ ", ) self.assertEqual(alignment.target.id, "A3QGB8_SHELP/1") self.assertEqual(alignment.target.seq[33:53], "LSLGMTRDQVMTLMGTADFN") self.assertEqual(alignment.target.annotations["hmm_name"], "PF11399.8") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF3192 ; Protein of unknown function (DUF3192)", ) self.assertEqual(alignment[0], "LSLGMTRDQVMTLMGTADFN") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCCCCCHHHHHHHhCCCcee ", ) self.assertEqual( str(alignment), """\ A3QGB8_SH 33 LSLGMTRDQVMTLMGTADFN 53 0 ...|.....|....|..... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 33, 53], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'S', 'L', 'G', 'M', 'T', 'R', 'D', 'Q', 'V', 'M', 'T', 'L', 'M', 'G', 'T', 'A', 'D', 'F', 'N'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 58.46) self.assertAlmostEqual(alignment.annotations["E-value"], 11) self.assertAlmostEqual(alignment.annotations["Score"], 31.36) self.assertAlmostEqual(alignment.annotations["Identities"], 35) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.376) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.400) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " l~~G~t~~eV~~~lG~P~~~ ", ) self.assertEqual(alignment.target.id, "5WAM_B") self.assertEqual(alignment.target.seq[29:49], "LRPGMTKDQVLLLLGSPILR") self.assertEqual(alignment.target.annotations["hmm_name"], "5WAM_B") self.assertEqual( alignment.target.annotations["hmm_description"], "Outer membrane protein assembly factor; beta-barrel assembly machinery, BAM complex; 2.45A {Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)}; Related PDB entries: 5WAM_A", ) self.assertEqual(alignment[0], "LRPGMTKDQVLLLLGSPILR") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCTTCBHHHHHHHHCCCSCC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHHCCCcee ", ) self.assertEqual( str(alignment), """\ 5WAM_B 29 LRPGMTKDQVLLLLGSPILR 49 0 ...|.....||..||||... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 29, 49], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'R', 'P', 'G', 'M', 'T', 'K', 'D', 'Q', 'V', 'L', 'L', 'L', 'L', 'G', 'S', 'P', 'I', 'L', 'R'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 57.72) self.assertAlmostEqual(alignment.annotations["E-value"], 1.6e02) self.assertAlmostEqual(alignment.annotations["Score"], 26.08) self.assertAlmostEqual(alignment.annotations["Identities"], 11) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.028) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.400) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEcCCcHHHHHHHHHHccCCcCcEEEEECCCCCcCCCEEEEeCCCCeEEEecCccceeeEEEEecCCCCEEEECCEEecCCCCCCcHHHHHHhhcCCCCCCccCcccEEEEEeCcEEEEee ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[18:139], "FTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQ", ) self.assertEqual( alignment[1], "FTLGMPLAQAVAILQKHCRIIKN--VQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLT-KVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNS----------AEQLFHLNFR--------GLSFSFQ", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " f~LG~sL~~vi~~Lr~~~~~~~~vel~Ys~~~pl~~~Ivi~L~~~GirL~Fd~~~QrL~lIEv~d~~~~~L~Y~~~~~~~~~~~ptf~~I~~~FGPTyPG~yd~~~~~Y~LsYpGisF~Fp ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " I~~G~s~~eV~~~lG~p~~~~~~~~~~~~W~~~~~~~~~~~v~f~~~~kv~~k~~~~~~~~~~~~~t~~~~~~i~~Gmt~~~V~~~lG~p~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~F~ ", ) self.assertEqual(alignment.target.id, "3GMX_B") self.assertEqual( alignment.target.seq[11:141], "IQFGMDRTLVWQLAGADQSCSDQVERIICYNNPDHYGPQGHFFFNAADKLIHKRQMELFPAPKPTMRLATYNKTQTGMTEAQFWAAVPSDTCSALAEQYPNWPATNGNLREYVCPSKAERFAPSAYFTFT", ) self.assertEqual(alignment.target.annotations["hmm_name"], "3GMX_B") self.assertEqual( alignment.target.annotations["hmm_description"], "BLP; 2-layer alpha/beta sandwich, PROTEIN BINDING; HET: ACT; 1.05A {Streptomyces clavuligerus} SCOP: d.98.1.0; Related PDB entries: 3GMX_A 3GMY_A 3GMY_B", ) self.assertEqual( alignment[0], "IQFGMDRTLVWQLAGADQSCSDQVERIICYNNPDHYGPQGHFFFNAAD----------KLIHKRQMELFPAPKPTMRLATYNKTQTGMTEAQFWAAVPS--DTCSALAEQYPNWPATNGNLREYVCPSKAERFAPSAYFTFT", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCTTCBHHHHHHHHTHHHHEEECSSCEEEESSSCTTSSEEEEEECTTSBEEEEEEESSSCCSSCCCCHHHHTTCCTTCBHHHHHHHSCGGGCEEEEEECTTTTSCTTCEEEEEEESSSSTTCCEEEEEEE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHhCCCceecCCceeEEEEcCCCCCcceEEEEEccCCEEEEEEecccCCCCCCCCCHHHHhhcCCCCCHHHHHHHcCCccceeceeccCCCCCCCCeEEEEEeCCCCCCCCCeEEEEEE ", ) self.assertEqual( str(alignment), """\ 3GMX_B 11 IQFGMDRTLVWQLAGADQSCSDQVERIICYNNPDHYGPQGHFFFNAAD----------KL 0 ...||..................--....|..................----------.| sp|Q9BSU1 18 FTLGMPLAQAVAILQKHCRIIKN--VQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRL 3GMX_B 61 IHKRQMELFPAPKPTMRLATYNKTQTGMTEAQFWAAVPS--DTCSALAEQYPNWPATNGN 60 .......|.-..|........|......|..|.......--......----------... sp|Q9BSU1 76 KVIEVCDLT-KVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNS----------AEQ 3GMX_B 119 LREYVCPSKAERFAPSAYFTFT 141 120 |......--------...|.|. 142 sp|Q9BSU1 125 LFHLNFR--------GLSFSFQ 139 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 11, 34, 36, 59, 59, 70, 71, 100, 100, 106, 116, 126, 134, 141], [ 18, 41, 41, 64, 74, 85, 85, 114, 116, 122, 122, 132, 132, 139]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'Q', 'F', 'G', 'M', 'D', 'R', 'T', 'L', 'V', 'W', 'Q', 'L', 'A', 'G', 'A', 'D', 'Q', 'S', 'C', 'S', 'D', 'Q', 'V', 'E', 'R', 'I', 'I', 'C', 'Y', 'N', 'N', 'P', 'D', 'H', 'Y', 'G', 'P', 'Q', 'G', 'H', 'F', 'F', 'F', 'N', 'A', 'A', 'D', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'K', 'L', 'I', 'H', 'K', 'R', 'Q', 'M', 'E', 'L', 'F', 'P', 'A', 'P', 'K', 'P', 'T', 'M', 'R', 'L', 'A', 'T', 'Y', 'N', 'K', 'T', 'Q', 'T', 'G', 'M', 'T', 'E', 'A', 'Q', 'F', 'W', 'A', 'A', 'V', 'P', 'S', '-', '-', 'D', 'T', 'C', 'S', 'A', 'L', 'A', 'E', 'Q', 'Y', 'P', 'N', 'W', 'P', 'A', 'T', 'N', 'G', 'N', 'L', 'R', 'E', 'Y', 'V', 'C', 'P', 'S', 'K', 'A', 'E', 'R', 'F', 'A', 'P', 'S', 'A', 'Y', 'F', 'T', 'F', 'T'], ['F', 'T', 'L', 'G', 'M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', 'K', 'N', '-', '-', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'C', 'D', 'L', 'T', '-', 'K', 'V', 'K', 'L', 'K', 'Y', 'C', 'G', 'V', 'H', 'F', 'N', 'S', 'Q', 'A', 'I', 'A', 'P', 'T', 'I', 'E', 'Q', 'I', 'D', 'Q', 'S', 'F', 'G', 'A', 'T', 'H', 'P', 'G', 'V', 'Y', 'N', 'S', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'E', 'Q', 'L', 'F', 'H', 'L', 'N', 'F', 'R', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'L', 'S', 'F', 'S', 'F', 'Q']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 57.07) self.assertAlmostEqual(alignment.annotations["E-value"], 24) self.assertAlmostEqual(alignment.annotations["Score"], 30.56) self.assertAlmostEqual(alignment.annotations["Identities"], 7) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.027) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 10.000) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEEEEeccccccccCCCCCcCCCCcCCccchhhHhhccceeecCCCCEEEEEEecCC ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[238:312], "VYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTN", ) self.assertEqual( alignment[1], "VYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTN", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~f~K~ddrm~IH~~~~~~~~~~~~~dyF~NYF~lG~DiLfd~~t~~v~KiILHtN ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~vG~t~~~v~~~~G~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fd~~~~~v~~I~~~~~ ", ) self.assertEqual(alignment.target.id, "U5LAW6_9BACI/1") self.assertEqual( alignment.target.seq[61:131], "FHIGQPVSEIYSSVFIDTNINFQYKGSSYRFELSEDDLNTRPLIKAGNIYAQLYIDRFTGELSSIRYMDA", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF14504.6") self.assertEqual( alignment.target.annotations["hmm_description"], "; CAP_assoc_N ; CAP-associated N-terminal", ) self.assertEqual( alignment[0], "FHIGQPVSEIYSSVFIDTNINFQYKGSSYRFELSEDD----LNTRPLIKAGNIYAQLYIDRFTGELSSIRYMDA", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ccCCCcHHHHHHhhcCCceEEEEEcCcEEEEEeCcchhccceeEEECCEEEEEEEECCCCEEEEEEEecH ", ) self.assertEqual( str(alignment), """\ U5LAW6_9B 61 FHIGQPVSEIYSSVFIDTNINFQYKGSSYRFELSEDD----LNTRPLIKAGNIYAQLYID 0 ...|.......|.....................|...----..................| sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFD U5LAW6_9B 117 RFTGELSSIRYMDA 131 60 ..|........... 74 sp|Q9BSU1 298 ANTHKVKKFVLHTN 312 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 61, 98, 98, 131], [238, 275, 279, 312]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['F', 'H', 'I', 'G', 'Q', 'P', 'V', 'S', 'E', 'I', 'Y', 'S', 'S', 'V', 'F', 'I', 'D', 'T', 'N', 'I', 'N', 'F', 'Q', 'Y', 'K', 'G', 'S', 'S', 'Y', 'R', 'F', 'E', 'L', 'S', 'E', 'D', 'D', '-', '-', '-', '-', 'L', 'N', 'T', 'R', 'P', 'L', 'I', 'K', 'A', 'G', 'N', 'I', 'Y', 'A', 'Q', 'L', 'Y', 'I', 'D', 'R', 'F', 'T', 'G', 'E', 'L', 'S', 'S', 'I', 'R', 'Y', 'M', 'D', 'A'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F', 'Y', 'K', 'S', 'E', 'D', 'K', 'M', 'K', 'I', 'H', 'S', 'P', 'S', 'P', 'H', 'K', 'Q', 'V', 'P', 'S', 'K', 'C', 'N', 'D', 'Y', 'F', 'F', 'N', 'Y', 'F', 'T', 'L', 'G', 'V', 'D', 'I', 'L', 'F', 'D', 'A', 'N', 'T', 'H', 'K', 'V', 'K', 'K', 'F', 'V', 'L', 'H', 'T', 'N']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 56.37) self.assertAlmostEqual(alignment.annotations["E-value"], 14) self.assertAlmostEqual(alignment.annotations["Score"], 29.98) self.assertAlmostEqual(alignment.annotations["Identities"], 30) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.380) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.700) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " l~~Gmtk~eV~~lLG~P~~~ ", ) self.assertEqual(alignment.target.id, "2YH9_C") self.assertEqual(alignment.target.seq[12:32], "IRVGMTQQQVAYALGTPLMS") self.assertEqual(alignment.target.annotations["hmm_name"], "2YH9_C") self.assertEqual( alignment.target.annotations["hmm_description"], "SMALL PROTEIN A; LIPOPROTEIN, 3D DOMAIN SWAP, MEMBRANE; HET: MSE; 1.8A {ESCHERICHIA COLI}; Related PDB entries: 2YH9_B 2YH9_A", ) self.assertEqual(alignment[0], "IRVGMTQQQVAYALGTPLMS") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCTTCBHHHHHHHHCSCSEE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHhCCCcee ", ) self.assertEqual( str(alignment), """\ 2YH9_C 12 IRVGMTQQQVAYALGTPLMS 32 0 ...|...|.|...||.|... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 12, 32], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'R', 'V', 'G', 'M', 'T', 'Q', 'Q', 'Q', 'V', 'A', 'Y', 'A', 'L', 'G', 'T', 'P', 'L', 'M', 'S'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 56.24) self.assertAlmostEqual(alignment.annotations["E-value"], 30) self.assertAlmostEqual(alignment.annotations["Score"], 29.96) self.assertAlmostEqual(alignment.annotations["Identities"], 11) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.142) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 10.000) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " ecCCHHHHHHHhcCCcEEEEeccccccccCCCCCcCCCCcCCccchhhHhhccceeecCCCCEEEEEEecCC ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[240:312], "FGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTN", ) self.assertEqual( alignment[1], "FGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFT-LGVDILFDANTHKVKKFVLHTN", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~G~T~QDVl~~LG~P~~~f~K~ddrm~IH~~~~~~~~~~~~~dyF~NYF~lG~DiLfd~~t~~v~KiILHtN ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "lG~~~~~v~~~lG~P~~~~~~~~g~~~~~Y~~~~~~~~~v~~~~~~v~~i~~~~~ ", ) self.assertEqual(alignment.target.id, "U5LAW6_9BACI/1") self.assertEqual( alignment.target.seq[0:55], "IGKNASDLQVLLGDPERKDPSEYGYEWWIYKKGTSQYVQAGVLDGRIVTLFATGP", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF14504.6") self.assertEqual( alignment.target.annotations["hmm_description"], "; CAP_assoc_N ; CAP-associated N-terminal", ) self.assertEqual( alignment[0], "IGKNASDLQVLLGDPERKDPSEYG------------------YEWWIYKKGTSQYVQAGVLDGRIVTLFATGP", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCCCHHHHHHHHCCCcEEeccccCCeEEEEecCCCcEEEEEEECCEEEEEEEcCC ", ) self.assertEqual( str(alignment), """\ U5LAW6_9B 0 IGKNASDLQVLLGDPERKDPSEYG------------------YEWWIYKKGTSQYVQAGV 0 .|....|....||.|.........------------------.....|..-......... sp|Q9BSU1 240 FGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFT-LGVDILFDA U5LAW6_9B 42 LDGRIVTLFATGP 55 60 ............. 73 sp|Q9BSU1 299 NTHKVKKFVLHTN 312 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 24, 24, 32, 33, 55], [240, 264, 282, 290, 290, 312]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'G', 'K', 'N', 'A', 'S', 'D', 'L', 'Q', 'V', 'L', 'L', 'G', 'D', 'P', 'E', 'R', 'K', 'D', 'P', 'S', 'E', 'Y', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'Y', 'E', 'W', 'W', 'I', 'Y', 'K', 'K', 'G', 'T', 'S', 'Q', 'Y', 'V', 'Q', 'A', 'G', 'V', 'L', 'D', 'G', 'R', 'I', 'V', 'T', 'L', 'F', 'A', 'T', 'G', 'P'], ['F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F', 'Y', 'K', 'S', 'E', 'D', 'K', 'M', 'K', 'I', 'H', 'S', 'P', 'S', 'P', 'H', 'K', 'Q', 'V', 'P', 'S', 'K', 'C', 'N', 'D', 'Y', 'F', 'F', 'N', 'Y', 'F', 'T', '-', 'L', 'G', 'V', 'D', 'I', 'L', 'F', 'D', 'A', 'N', 'T', 'H', 'K', 'V', 'K', 'K', 'F', 'V', 'L', 'H', 'T', 'N']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 56.21) self.assertAlmostEqual(alignment.annotations["E-value"], 14) self.assertAlmostEqual(alignment.annotations["Score"], 31.47) self.assertAlmostEqual(alignment.annotations["Identities"], 40) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.433) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.400) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " I~~GmTk~qV~~~lG~P~~~ ", ) self.assertEqual(alignment.target.id, "4DM5_A") self.assertEqual(alignment.target.seq[23:43], "VEKGMSQQEVLRIGGTPSGT") self.assertEqual(alignment.target.annotations["hmm_name"], "4DM5_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Osmotically inducible lipoprotein OsmE; lipoprotein, UNKNOWN FUNCTION; HET: MSE; 1.5A {Pseudomonas aeruginosa PAO1}; Related PDB entries: 4DM5_C 4DM5_D 4DM5_B", ) self.assertEqual(alignment[0], "VEKGMSQQEVLRIGGTPSGT") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCTTCBHHHHHHHHCSCSEE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHhCCCCee ", ) self.assertEqual( str(alignment), """\ 4DM5_A 23 VEKGMSQQEVLRIGGTPSGT 43 0 |..|.|.|.||...|.|... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 23, 43], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['V', 'E', 'K', 'G', 'M', 'S', 'Q', 'Q', 'E', 'V', 'L', 'R', 'I', 'G', 'G', 'T', 'P', 'S', 'G', 'T'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 56.09) self.assertAlmostEqual(alignment.annotations["E-value"], 77) self.assertAlmostEqual(alignment.annotations["Score"], 27.35) self.assertAlmostEqual(alignment.annotations["Identities"], 22) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.238) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 10.000) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CCCCccEEcCCcHHHHHHHHHHccCCcCcEEEEECCCCCcCCCEEEEeCCCCeEEEecCccceeeEEEEec ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[12:83], "GNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCD", ) self.assertEqual( alignment[1], "GNEQWEFTLGMPLAQAVAILQKHCRI-----IKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCD", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " G~~~~~f~LG~sL~~vi~~Lr~~~~~~~~vel~Ys~~~pl~~~Ivi~L~~~GirL~Fd~~~QrL~lIEv~d ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " gi~vG~t~~~v~~~~G~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fd~~~~~v~~I~~~~ ", ) self.assertEqual(alignment.target.id, "U5LAW6_9BACI/1") self.assertEqual( alignment.target.seq[60:130], "PFHIGQPVSEIYSSVFIDTNINFQYKGSSYRFELSEDDLNTRPLIKAGNIYAQLYIDRFTGELSSIRYMD", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF14504.6") self.assertEqual( alignment.target.annotations["hmm_description"], "; CAP_assoc_N ; CAP-associated N-terminal", ) self.assertEqual( alignment[0], "P-----FHIGQPVSEIYSSVFIDTNINFQYKGSSYRFELSEDDLNTRPLIKA-GNIYAQLYIDRFTGELSSIRYMD", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CccCCCcHHHHHHhhcCCceEEEEEcCcEEEEEeCcchhccceeEEECCEEEEEEEECCCCEEEEEEEec ", ) self.assertEqual( str(alignment), """\ U5LAW6_9B 60 P-----FHIGQPVSEIYSSVFIDTNINFQYKGSSYRFELSEDDLNTRPLIKA-GNIYAQL 0 .-----|..|.|.............|-----........||.......||..-......| sp|Q9BSU1 12 GNEQWEFTLGMPLAQAVAILQKHCRI-----IKNVQVLYSEQSPLSHDLILNLTQDGIKL U5LAW6_9B 114 YIDRFTGELSSIRYMD 130 60 ..|.|...|..|...| 76 sp|Q9BSU1 67 MFDAFNQRLKVIEVCD 83 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 60, 61, 61, 81, 86, 107, 107, 130], [ 12, 13, 18, 38, 38, 59, 60, 83]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['P', '-', '-', '-', '-', '-', 'F', 'H', 'I', 'G', 'Q', 'P', 'V', 'S', 'E', 'I', 'Y', 'S', 'S', 'V', 'F', 'I', 'D', 'T', 'N', 'I', 'N', 'F', 'Q', 'Y', 'K', 'G', 'S', 'S', 'Y', 'R', 'F', 'E', 'L', 'S', 'E', 'D', 'D', 'L', 'N', 'T', 'R', 'P', 'L', 'I', 'K', 'A', '-', 'G', 'N', 'I', 'Y', 'A', 'Q', 'L', 'Y', 'I', 'D', 'R', 'F', 'T', 'G', 'E', 'L', 'S', 'S', 'I', 'R', 'Y', 'M', 'D'], ['G', 'N', 'E', 'Q', 'W', 'E', 'F', 'T', 'L', 'G', 'M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', '-', '-', '-', '-', '-', 'I', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'C', 'D']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 53.82) self.assertAlmostEqual(alignment.annotations["E-value"], 2.4e02) self.assertAlmostEqual(alignment.annotations["Score"], 24.83) self.assertAlmostEqual(alignment.annotations["Identities"], 8) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.090) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.400) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " ccccCCCCccEEcCCcHHHHHHHHHHccCCcCcEEEEECCCCCcCCCEEEEeCCCCeEEEecCccceeeEEEEecCCCCEEEECCEEecCCCCCCcHHHHHHhhcCCCCCCccCcccEEEEEeCcEEEEeeCcccCCCCccCCCcccccccCCCCCCCeEEEEEEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[8:174], "ERSLGNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKRMYIY", ) self.assertEqual( alignment[1], "ERSLGNEQWEFTLGMP-LAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNF-RG----LSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKRMYIY", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " g~~LG~~~~~f~LG~sL~~vi~~Lr~~~~~~~~vel~Ys~~~pl~~~Ivi~L~~~GirL~Fd~~~QrL~lIEv~d~~~~~L~Y~~~~~~~~~~~ptf~~I~~~FGPTyPG~yd~~~~~Y~LsYpGisF~Fpi~~~~~~~~~~~~~~~~l~~l~~~~~~~~s~i~If ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " Gk~~g~~~~lG~s~~~~V~~~~G~P~~~~~~~~~~g~~~~Y~~~~~~f~~~~~~~v~~i~~~~~~~~~lt~~~v~~~LG~P~~~~~~~~~~~~~Y~~g~~y~L~f~~~~~~~~~~~~~v~~i~v~", ) self.assertEqual(alignment.target.id, "R4K5N0_CLOPA/8") self.assertEqual( alignment.target.seq[10:135], "GKVFNSDFPAKDTNIDSVESKWGKADNSEWVASAKGLYSTYSKHNIVFGSNKGGQIFEVRSLDKQLGNIYLSMVKDKLGTPQHDVKVNGEEIIGYKMGNDFKILFVFPEPTNQHANPIMSHYSVL", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF14172.6") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF4309 ; Domain of unknown function (DUF4309)", ) self.assertEqual( alignment[0], "GKVFNS---DFPAKDTNIDSVESKWGK------ADNSEWVASA---KGLYSTYSKHNIVFGSNKGG-QIFEVRSLDKQLGN--------------IYLSMVKDKLG--TPQHDVKVNGEEIIGYKMGNDFKILFVFPEPTNQ------------------HANPIMSHYSVL", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCCCCcHHHHHHHhCCCCceehhhhcCceeEEecCceEEEEECCCCeEEEEEEechhhcCCCHHHHHHHhCCCcEEEEECCEEEEEEEeCCCEEEEEEeCCCCCCCCCCeeeEEEeC", ) self.assertEqual( str(alignment), """\ R4K5N0_CL 10 GKVFNS---DFPAKDTNIDSVESKWGK------ADNSEWVASA---KGLYSTYSKHNIVF 0 ......---.|.....-.........|------..........---..|........|.. sp|Q9BSU1 8 ERSLGNEQWEFTLGMP-LAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKL R4K5N0_CL 58 GSNKGG-QIFEVRSLDKQLGN--------------IYLSMVKDKLG--TPQHDVKVNGEE 60 ......-........|.....--------------..........|--.|.......... sp|Q9BSU1 67 MFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLF R4K5N0_CL 101 IIGYKMGNDFKILFVFPEPTNQ------------------HANPIMSHYSVL 135 120 ....-.|----..|.|......------------------............ 172 sp|Q9BSU1 127 HLNF-RG----LSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKRMYIY 174 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 10, 16, 16, 23, 24, 34, 34, 44, 44, 64, 64, 78, 78, 89, 89, 105, 106, 108, 112, 123, 123, 135], [ 8, 14, 17, 24, 24, 34, 40, 50, 53, 73, 74, 88, 102, 113, 115, 131, 131, 133, 133, 144, 162, 174]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'K', 'V', 'F', 'N', 'S', '-', '-', '-', 'D', 'F', 'P', 'A', 'K', 'D', 'T', 'N', 'I', 'D', 'S', 'V', 'E', 'S', 'K', 'W', 'G', 'K', '-', '-', '-', '-', '-', '-', 'A', 'D', 'N', 'S', 'E', 'W', 'V', 'A', 'S', 'A', '-', '-', '-', 'K', 'G', 'L', 'Y', 'S', 'T', 'Y', 'S', 'K', 'H', 'N', 'I', 'V', 'F', 'G', 'S', 'N', 'K', 'G', 'G', '-', 'Q', 'I', 'F', 'E', 'V', 'R', 'S', 'L', 'D', 'K', 'Q', 'L', 'G', 'N', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'I', 'Y', 'L', 'S', 'M', 'V', 'K', 'D', 'K', 'L', 'G', '-', '-', 'T', 'P', 'Q', 'H', 'D', 'V', 'K', 'V', 'N', 'G', 'E', 'E', 'I', 'I', 'G', 'Y', 'K', 'M', 'G', 'N', 'D', 'F', 'K', 'I', 'L', 'F', 'V', 'F', 'P', 'E', 'P', 'T', 'N', 'Q', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'H', 'A', 'N', 'P', 'I', 'M', 'S', 'H', 'Y', 'S', 'V', 'L'], ['E', 'R', 'S', 'L', 'G', 'N', 'E', 'Q', 'W', 'E', 'F', 'T', 'L', 'G', 'M', 'P', '-', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'C', 'D', 'L', 'T', 'K', 'V', 'K', 'L', 'K', 'Y', 'C', 'G', 'V', 'H', 'F', 'N', 'S', 'Q', 'A', 'I', 'A', 'P', 'T', 'I', 'E', 'Q', 'I', 'D', 'Q', 'S', 'F', 'G', 'A', 'T', 'H', 'P', 'G', 'V', 'Y', 'N', 'S', 'A', 'E', 'Q', 'L', 'F', 'H', 'L', 'N', 'F', '-', 'R', 'G', '-', '-', '-', '-', 'L', 'S', 'F', 'S', 'F', 'Q', 'L', 'D', 'S', 'W', 'T', 'E', 'A', 'P', 'K', 'Y', 'E', 'P', 'N', 'F', 'A', 'H', 'G', 'L', 'A', 'S', 'L', 'Q', 'I', 'P', 'H', 'G', 'A', 'T', 'V', 'K', 'R', 'M', 'Y', 'I', 'Y']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 52.88) self.assertAlmostEqual(alignment.annotations["E-value"], 16) self.assertAlmostEqual(alignment.annotations["Score"], 31.41) self.assertAlmostEqual(alignment.annotations["Identities"], 20) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.320) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.800) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " I~~G~t~~~V~~~lG~P~~~ ", ) self.assertEqual(alignment.target.id, "B5GLC0_STRC2/3") self.assertEqual(alignment.target.seq[7:27], "IQFGMDRTLVWQLAGADQSC") self.assertEqual(alignment.target.annotations["hmm_name"], "PF07467.11") self.assertEqual( alignment.target.annotations["hmm_description"], "; BLIP ; Beta-lactamase inhibitor (BLIP)", ) self.assertEqual(alignment[0], "IQFGMDRTLVWQLAGADQSC") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHHCCCcee ", ) self.assertEqual( str(alignment), """\ B5GLC0_ST 7 IQFGMDRTLVWQLAGADQSC 27 0 ..||.....|....|..... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 7, 27], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'Q', 'F', 'G', 'M', 'D', 'R', 'T', 'L', 'V', 'W', 'Q', 'L', 'A', 'G', 'A', 'D', 'Q', 'S', 'C'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 50.88) self.assertAlmostEqual(alignment.annotations["E-value"], 27) self.assertAlmostEqual(alignment.annotations["Score"], 28.63) self.assertAlmostEqual(alignment.annotations["Identities"], 19) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.145) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.700) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEEEEecccc ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:265], "VYFGDSCQDVLSMLGSPHKVFYKSEDK") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKVFYKSEDK") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~f~K~ddr ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " V~~Gds~~~Vl~~cG~P~~~~~~~~~~ ", ) self.assertEqual(alignment.target.id, "B3PEX3_CELJU/2") self.assertEqual(alignment.target.seq[10:37], "TQTGDTKAEVIAKCGDPVFTDHYCAPM") self.assertEqual(alignment.target.annotations["hmm_name"], "PF11006.8") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF2845 ; Protein of unknown function (DUF2845)", ) self.assertEqual(alignment[0], "TQTGDTKAEVIAKCGDPVFTDHYCAPM") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCCCCCHHHHHHHhCCCcEEEeEeeec ", ) self.assertEqual( str(alignment), """\ B3PEX3_CE 10 TQTGDTKAEVIAKCGDPVFTDHYCAPM 37 0 ...||....|....|.|.......... 27 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKVFYKSEDK 265 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 10, 37], [238, 265]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'Q', 'T', 'G', 'D', 'T', 'K', 'A', 'E', 'V', 'I', 'A', 'K', 'C', 'G', 'D', 'P', 'V', 'F', 'T', 'D', 'H', 'Y', 'C', 'A', 'P', 'M'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F', 'Y', 'K', 'S', 'E', 'D', 'K']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 49.44) self.assertAlmostEqual(alignment.annotations["E-value"], 1.1e02) self.assertAlmostEqual(alignment.annotations["Score"], 27.28) self.assertAlmostEqual(alignment.annotations["Identities"], 9) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.155) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EeccccccCCCCccEEcCCcHHHHHHHHHHccCCcCcEEEEECCCCCcCCCEEEEeCCCCeEEEecCccceeeEEEEecCCCCEEEECCEEecCCCCCCcHHHHHHhhcCCCCCCccCcccEEEEEeCcEEEEe ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[4:138], "EVVPERSLGNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSF", ) self.assertEqual( alignment[1], "EVVPERSLGNEQWEFTLGMPLAQAVAILQKHCRIIKNV-------QVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKV-KLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAE----QLFHLNFR----------GLSFSF", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~i~Pg~~LG~~~~~f~LG~sL~~vi~~Lr~~~~~~~~vel~Ys~~~pl~~~Ivi~L~~~GirL~Fd~~~QrL~lIEv~d~~~~~L~Y~~~~~~~~~~~ptf~~I~~~FGPTyPG~yd~~~~~Y~LsYpGisF~F ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~i~~~~~~~~~~~G~t~~eV~~~lG~p~~~~~~~~~~~~~~~~~w~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~i~~G~t~~eV~~~lG~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~F ", ) self.assertEqual(alignment.target.id, "Q8DTX1_STRMU/4") self.assertEqual( alignment.target.seq[10:146], "KIKVTTDQNHFSGGTSIEQLKQWFGDPNKSEQRNAGNITLDSYTWVKDGAVINAQLYKNSTVARSISNFSFSREAKIGKEDYDELKIGESYKKVVEKLGEPDVLSQSMSSDKEEMQTVWSSGIKTKSSSATIELYF", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF12978.7") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF3862 ; Domain of Unknown Function with PDB structure (DUF3862)", ) self.assertEqual( alignment[0], "KIKVTTDQNH----FSGGTSIEQLKQWFGDPNKSEQRNAGNITLDSYTWVK------------DGAVINAQLY--KNSTVARSISNFSFSREAKIGKEDYDELKIGESYKKVVEKLG--EPDVLSQSMSSDKEEMQTVWSSGIKTKSSSATIELYF", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ceeecCCcccCCCCCCHHHHHHHHCCCceEEeeeeCCeEEEEEEEEeCCeEEEEEEECCEEEEEEEEeceecCCCCCCHHHHHhcCCCCCHHHHHHHHCCCCeeEEEeeCCceEEEEEEEecccCCCCCcEEEEEE ", ) self.assertEqual( str(alignment), """\ Q8DTX1_ST 10 KIKVTTDQNH----FSGGTSIEQLKQWFGDPNKSEQRNAGNITLDSYTWVK--------- 0 ..........----|..|....|...............-------......--------- sp|Q9BSU1 4 EVVPERSLGNEQWEFTLGMPLAQAVAILQKHCRIIKNV-------QVLYSEQSPLSHDLI Q8DTX1_ST 57 ---DGAVINAQLY--KNSTVARSISNFSFSREAKIGKEDYDELKIGESYKKVVEKLG--E 60 ---....|.....--...............-..|..........|...........|--. sp|Q9BSU1 57 LNLTQDGIKLMFDAFNQRLKVIEVCDLTKV-KLKYCGVHFNSQAIAPTIEQIDQSFGATH Q8DTX1_ST 110 PDVLSQSMSSDKEEMQTVWSSGIKTKSSSATIELYF 146 120 |.|.....----........----------.....| 156 sp|Q9BSU1 116 PGVYNSAE----QLFHLNFR----------GLSFSF 138 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 10, 20, 20, 44, 51, 57, 57, 67, 67, 82, 83, 109, 109, 118, 122, 130, 140, 146], [ 4, 14, 18, 42, 42, 48, 60, 70, 72, 87, 87, 113, 115, 124, 124, 132, 132, 138]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'I', 'K', 'V', 'T', 'T', 'D', 'Q', 'N', 'H', '-', '-', '-', '-', 'F', 'S', 'G', 'G', 'T', 'S', 'I', 'E', 'Q', 'L', 'K', 'Q', 'W', 'F', 'G', 'D', 'P', 'N', 'K', 'S', 'E', 'Q', 'R', 'N', 'A', 'G', 'N', 'I', 'T', 'L', 'D', 'S', 'Y', 'T', 'W', 'V', 'K', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'D', 'G', 'A', 'V', 'I', 'N', 'A', 'Q', 'L', 'Y', '-', '-', 'K', 'N', 'S', 'T', 'V', 'A', 'R', 'S', 'I', 'S', 'N', 'F', 'S', 'F', 'S', 'R', 'E', 'A', 'K', 'I', 'G', 'K', 'E', 'D', 'Y', 'D', 'E', 'L', 'K', 'I', 'G', 'E', 'S', 'Y', 'K', 'K', 'V', 'V', 'E', 'K', 'L', 'G', '-', '-', 'E', 'P', 'D', 'V', 'L', 'S', 'Q', 'S', 'M', 'S', 'S', 'D', 'K', 'E', 'E', 'M', 'Q', 'T', 'V', 'W', 'S', 'S', 'G', 'I', 'K', 'T', 'K', 'S', 'S', 'S', 'A', 'T', 'I', 'E', 'L', 'Y', 'F'], ['E', 'V', 'V', 'P', 'E', 'R', 'S', 'L', 'G', 'N', 'E', 'Q', 'W', 'E', 'F', 'T', 'L', 'G', 'M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', 'K', 'N', 'V', '-', '-', '-', '-', '-', '-', '-', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'C', 'D', 'L', 'T', 'K', 'V', '-', 'K', 'L', 'K', 'Y', 'C', 'G', 'V', 'H', 'F', 'N', 'S', 'Q', 'A', 'I', 'A', 'P', 'T', 'I', 'E', 'Q', 'I', 'D', 'Q', 'S', 'F', 'G', 'A', 'T', 'H', 'P', 'G', 'V', 'Y', 'N', 'S', 'A', 'E', '-', '-', '-', '-', 'Q', 'L', 'F', 'H', 'L', 'N', 'F', 'R', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'L', 'S', 'F', 'S', 'F']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 48.69) self.assertAlmostEqual(alignment.annotations["E-value"], 1.6e02) self.assertAlmostEqual(alignment.annotations["Score"], 25.16) self.assertAlmostEqual(alignment.annotations["Identities"], 18) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.331) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 4.200) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CcHHHHHHHHHHccCCcCcEEEEECCCCCcCCCEEEEeCCCCeEEEecCccceeeEEEEe ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[22:82], "MPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVC", ) self.assertEqual( alignment[1], "MPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNL----TQDGIKLMFDAFNQRLK-VIEVC", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~sL~~vi~~Lr~~~~~~~~vel~Ys~~~pl~~~Ivi~L~~~GirL~Fd~~~QrL~lIEv~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " m~~dE~ieYik~nVk~~D~lEisynRvf~pGeVl~i~~~~~~~~~~~~v~l~l~ge~~~~~veiD ", ) self.assertEqual(alignment.target.id, "A5UN43_METS3/2") self.assertEqual( alignment.target.seq[4:69], "LTPDKAVEYLKDNVKIHDNLEISYNRIFGSGEVLNMDFSEYFGKPGFKMLLSLDGDSINPTIEID", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF09870.9") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF2097 ; Uncharacterized protein conserved in archaea (DUF2097)", ) self.assertEqual( alignment[0], "LTPDKAVEYLKDNVKIHDNLEISYNRIFGSGEVLNMDFSEYFGKPGFKMLLSLDGDSINPTIEID", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCHHHHHHHHHHhCCccCeEEEEeceeecceeEEEEeeceecCCCeEEEEEEeCCCeecceEEEe ", ) self.assertEqual( str(alignment), """\ A5UN43_ME 4 LTPDKAVEYLKDNVKIHDNLEISYNRIFGSGEVLNMDFSEYFGKPGFKMLLSLDGDSINP 0 .....||..|.....|..|....|.........|....----...|.|...........- sp|Q9BSU1 22 MPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNL----TQDGIKLMFDAFNQRLK- A5UN43_ME 64 TIEID 69 60 .||.. 65 sp|Q9BSU1 77 VIEVC 82 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 4, 42, 46, 63, 64, 69], [22, 60, 60, 77, 77, 82]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'T', 'P', 'D', 'K', 'A', 'V', 'E', 'Y', 'L', 'K', 'D', 'N', 'V', 'K', 'I', 'H', 'D', 'N', 'L', 'E', 'I', 'S', 'Y', 'N', 'R', 'I', 'F', 'G', 'S', 'G', 'E', 'V', 'L', 'N', 'M', 'D', 'F', 'S', 'E', 'Y', 'F', 'G', 'K', 'P', 'G', 'F', 'K', 'M', 'L', 'L', 'S', 'L', 'D', 'G', 'D', 'S', 'I', 'N', 'P', 'T', 'I', 'E', 'I', 'D'], ['M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', '-', '-', '-', '-', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', '-', 'V', 'I', 'E', 'V', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 43.68) self.assertAlmostEqual(alignment.annotations["E-value"], 24) self.assertAlmostEqual(alignment.annotations["Score"], 30.46) self.assertAlmostEqual(alignment.annotations["Identities"], 35) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.526) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.300) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " I~~G~Tk~eV~~~LG~P~~~ ", ) self.assertEqual(alignment.target.id, "2PXG_A") self.assertEqual(alignment.target.seq[25:45], "LQVGQSKQQVSALLGTPSIP") self.assertEqual(alignment.target.annotations["hmm_name"], "2PXG_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Outer membrane protein; two layer alpha/beta plait, two; NMR {Xanthomonas axonopodis pv. citri}", ) self.assertEqual(alignment[0], "LQVGQSKQQVSALLGTPSIP") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " TCCCSCHHHHHHHHTSCCCC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHhCCCccC ", ) self.assertEqual( str(alignment), """\ 2PXG_A 25 LQVGQSKQQVSALLGTPSIP 45 0 ...|.|.|.|...||.|... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 25, 45], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'Q', 'V', 'G', 'Q', 'S', 'K', 'Q', 'Q', 'V', 'S', 'A', 'L', 'L', 'G', 'T', 'P', 'S', 'I', 'P'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 42.97) self.assertAlmostEqual(alignment.annotations["E-value"], 29) self.assertAlmostEqual(alignment.annotations["Score"], 30.94) self.assertAlmostEqual(alignment.annotations["Identities"], 20) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.320) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.400) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " I~~G~s~~eV~~~lG~p~~~ ", ) self.assertEqual(alignment.target.id, "3GMX_B") self.assertEqual(alignment.target.seq[11:31], "IQFGMDRTLVWQLAGADQSC") self.assertEqual(alignment.target.annotations["hmm_name"], "3GMX_B") self.assertEqual( alignment.target.annotations["hmm_description"], "BLP; 2-layer alpha/beta sandwich, PROTEIN BINDING; HET: ACT; 1.05A {Streptomyces clavuligerus} SCOP: d.98.1.0; Related PDB entries: 3GMX_A 3GMY_A 3GMY_B", ) self.assertEqual(alignment[0], "IQFGMDRTLVWQLAGADQSC") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCTTCBHHHHHHHHTHHHHE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHhCCCcee ", ) self.assertEqual( str(alignment), """\ 3GMX_B 11 IQFGMDRTLVWQLAGADQSC 31 0 ..||.....|....|..... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 11, 31], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'Q', 'F', 'G', 'M', 'D', 'R', 'T', 'L', 'V', 'W', 'Q', 'L', 'A', 'G', 'A', 'D', 'Q', 'S', 'C'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 41.38) self.assertAlmostEqual(alignment.annotations["E-value"], 33) self.assertAlmostEqual(alignment.annotations["Score"], 29.00) self.assertAlmostEqual(alignment.annotations["Identities"], 30) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.380) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.900) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " l~~G~t~~eV~~~lG~P~~~ ", ) self.assertEqual(alignment.target.id, "5D0O_E") self.assertEqual(alignment.target.seq[45:65], "IRVGMTQQQVAYALGTPLMS") self.assertEqual(alignment.target.annotations["hmm_name"], "5D0O_E") self.assertEqual( alignment.target.annotations["hmm_description"], "Outer membrane protein assembly factor; E.coli, Bacterial outer membrane beta; 2.9A {Escherichia coli}; Related PDB entries: 5D0Q_E 5D0Q_I", ) self.assertEqual(alignment[0], "IRVGMTQQQVAYALGTPLMS") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCSSCBHHHHHHHHCCCSBC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHhCCCcee ", ) self.assertEqual( str(alignment), """\ 5D0O_E 45 IRVGMTQQQVAYALGTPLMS 65 0 ...|...|.|...||.|... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 45, 65], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'R', 'V', 'G', 'M', 'T', 'Q', 'Q', 'Q', 'V', 'A', 'Y', 'A', 'L', 'G', 'T', 'P', 'L', 'M', 'S'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 39.07) self.assertAlmostEqual(alignment.annotations["E-value"], 83) self.assertAlmostEqual(alignment.annotations["Score"], 29.23) self.assertAlmostEqual(alignment.annotations["Identities"], 12) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.176) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.500) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEEEEeccccccccCCCCCcCCCCcCCccchhhHhhccceeecCCCCEEEEEEec ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[238:310], "VYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLH", ) self.assertEqual( alignment[1], "VYF---------GDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLH", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~f~K~ddrm~IH~~~~~~~~~~~~~dyF~NYF~lG~DiLfd~~t~~v~KiILH ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " I~~g~~~~~~~~Gmt~~eV~~ilG~P~~~~~~~~~~~~~~~~~W~~~~~~i~v~F~~~kv~~k~~~~ ", ) self.assertEqual(alignment.target.id, "3D4E_A") self.assertEqual( alignment.target.seq[30:97], "IKVTTDQNHFSGGTSIEQLKQWFGDPNKSEQRNAGNITLDSYTWVKDGAVINAQLYKNSTVARSISN", ) self.assertEqual(alignment.target.annotations["hmm_name"], "3D4E_A") self.assertEqual( alignment.target.annotations["hmm_description"], "putative beta-lactamase inhibitor protein; NP_721579.1, putative beta-lactamase inhibitor protein; HET: EDO, MSE; 1.4A {Streptococcus mutans}", ) self.assertEqual( alignment[0], "IKVTTDQNHFSGGTSIEQLKQWFGDPNKSEQRNAG-------------NITLDSYTWVKDGAVINAQLY-KNSTVARSISN", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCCCCCTTTCCSSCCHHHHHHHHCSCSEEEEEEETTEEEEEEEEEETTEEEEEEEETTEEEEEEEES ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " eeecCCccCCCCCCCHHHHHHHHCCCceeEEEeeCCEEEEEEEEEeCCeEEEEEEECCeEEEeeeec ", ) self.assertEqual( str(alignment), """\ 3D4E_A 30 IKVTTDQNHFSGGTSIEQLKQWFGDPNKSEQRNAG-------------NITLDSYTWVKD 0 ...---------|.|........|.|.|.......-------------......|..... sp|Q9BSU1 238 VYF---------GDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYF 3D4E_A 77 GAVINAQLY-KNSTVARSISN 97 60 .........-....|...... 81 sp|Q9BSU1 289 TLGVDILFDANTHKVKKFVLH 310 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 30, 33, 42, 65, 65, 86, 86, 97], [238, 241, 241, 264, 277, 298, 299, 310]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'K', 'V', 'T', 'T', 'D', 'Q', 'N', 'H', 'F', 'S', 'G', 'G', 'T', 'S', 'I', 'E', 'Q', 'L', 'K', 'Q', 'W', 'F', 'G', 'D', 'P', 'N', 'K', 'S', 'E', 'Q', 'R', 'N', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'N', 'I', 'T', 'L', 'D', 'S', 'Y', 'T', 'W', 'V', 'K', 'D', 'G', 'A', 'V', 'I', 'N', 'A', 'Q', 'L', 'Y', '-', 'K', 'N', 'S', 'T', 'V', 'A', 'R', 'S', 'I', 'S', 'N'], ['V', 'Y', 'F', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F', 'Y', 'K', 'S', 'E', 'D', 'K', 'M', 'K', 'I', 'H', 'S', 'P', 'S', 'P', 'H', 'K', 'Q', 'V', 'P', 'S', 'K', 'C', 'N', 'D', 'Y', 'F', 'F', 'N', 'Y', 'F', 'T', 'L', 'G', 'V', 'D', 'I', 'L', 'F', 'D', 'A', 'N', 'T', 'H', 'K', 'V', 'K', 'K', 'F', 'V', 'L', 'H']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 36.91) self.assertAlmostEqual(alignment.annotations["E-value"], 3e02) self.assertAlmostEqual(alignment.annotations["Score"], 25.55) self.assertAlmostEqual(alignment.annotations["Identities"], 10) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.142) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.500) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEcCCcHHHHHHHHHHccCCcCcEEEEECCCCCcCCCEEEEeCCCCeEEEecCccceeeEEEEecCCCCEEEECCEEecCCCCCCcHHHHHHhhcCCCCCCccCcccEEEEEeCcEEEEee ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[18:139], "FTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQ", ) self.assertEqual( alignment[1], "FTL---------GMPLAQAVAILQKHCRII-------KNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTK-VKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQ----LFHLNF----------RGLSFSFQ", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " f~LG~sL~~vi~~Lr~~~~~~~~vel~Ys~~~pl~~~Ivi~L~~~GirL~Fd~~~QrL~lIEv~d~~~~~L~Y~~~~~~~~~~~ptf~~I~~~FGPTyPG~yd~~~~~Y~LsYpGisF~Fp ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " I~~g~~~~~~~~Gmt~~eV~~ilG~P~~~~~~~~~~~~~~~~~W~~~~~~i~v~F~~~kv~~k~~~~~~~~~~~~it~~~~~~I~~Gmt~~eV~~~lG~p~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~i~~~F~ ", ) self.assertEqual(alignment.target.id, "3D4E_A") self.assertEqual( alignment.target.seq[30:166], "IKVTTDQNHFSGGTSIEQLKQWFGDPNKSEQRNAGNITLDSYTWVKDGAVINAQLYKNSTVARSISNFSFSREAKIGKEDYDELKIGESYKKIVEKLGEPDVLSQSMSSDKEEMQTVWSSGIKTKSSSATIELYFE", ) self.assertEqual(alignment.target.annotations["hmm_name"], "3D4E_A") self.assertEqual( alignment.target.annotations["hmm_description"], "putative beta-lactamase inhibitor protein; NP_721579.1, putative beta-lactamase inhibitor protein; HET: EDO, MSE; 1.4A {Streptococcus mutans}", ) self.assertEqual( alignment[0], "IKVTTDQNHFSGGTSIEQLKQWFGDPNKSEQRNAGNITLDSYTWVK------------DGAVINAQLY--KNSTVARSISNFSFSREAKIGKEDYDELKIGESYKKIVEKLGE--PDVLSQSMSSDKEEMQTVWSSGIKTKSSSATIELYFE", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCCCCCTTTCCSSCCHHHHHHHHCSCSEEEEEEETTEEEEEEEEEETTEEEEEEEETTEEEEEEEESCCCCCCCCBCHHHHHHCCTTCBHHHHHHHHCCCSEEEEEECSSCEEEEEEECSSBCSSCTTCEEEEEEE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " eeecCCccCCCCCCCHHHHHHHHCCCceeEEEeeCCEEEEEEEEEeCCeEEEEEEECCeEEEeeeecCccccCCCCCHHHHHHCCCCCCHHHHHHHHCCCceeeeecCCCceEEEEEEEcCCcCCCCccEEEEEEE ", ) self.assertEqual( str(alignment), """\ 3D4E_A 30 IKVTTDQNHFSGGTSIEQLKQWFGDPNKSEQRNAGNITLDSYTWVK------------DG 0 ...---------|....|............-------.........------------.. sp|Q9BSU1 18 FTL---------GMPLAQAVAILQKHCRII-------KNVQVLYSEQSPLSHDLILNLTQ 3D4E_A 78 AVINAQLY--KNSTVARSISNFSFSREAKIGKEDYDELKIGESYKKIVEKLGE--PDVLS 60 ..|.....--..............-...|..........|......|....|.--|.|.. sp|Q9BSU1 62 DGIKLMFDAFNQRLKVIEVCDLTK-VKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYN 3D4E_A 134 QSMSSDKEEMQTVWSSGIKTKSSSATIELYFE 166 120 ....----......----------......|. 152 sp|Q9BSU1 121 SAEQ----LFHLNF----------RGLSFSFQ 139 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 30, 33, 42, 60, 67, 76, 76, 86, 86, 100, 101, 129, 129, 138, 142, 148, 158, 166], [ 18, 21, 21, 39, 39, 48, 60, 70, 72, 86, 86, 114, 116, 125, 125, 131, 131, 139]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'K', 'V', 'T', 'T', 'D', 'Q', 'N', 'H', 'F', 'S', 'G', 'G', 'T', 'S', 'I', 'E', 'Q', 'L', 'K', 'Q', 'W', 'F', 'G', 'D', 'P', 'N', 'K', 'S', 'E', 'Q', 'R', 'N', 'A', 'G', 'N', 'I', 'T', 'L', 'D', 'S', 'Y', 'T', 'W', 'V', 'K', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'D', 'G', 'A', 'V', 'I', 'N', 'A', 'Q', 'L', 'Y', '-', '-', 'K', 'N', 'S', 'T', 'V', 'A', 'R', 'S', 'I', 'S', 'N', 'F', 'S', 'F', 'S', 'R', 'E', 'A', 'K', 'I', 'G', 'K', 'E', 'D', 'Y', 'D', 'E', 'L', 'K', 'I', 'G', 'E', 'S', 'Y', 'K', 'K', 'I', 'V', 'E', 'K', 'L', 'G', 'E', '-', '-', 'P', 'D', 'V', 'L', 'S', 'Q', 'S', 'M', 'S', 'S', 'D', 'K', 'E', 'E', 'M', 'Q', 'T', 'V', 'W', 'S', 'S', 'G', 'I', 'K', 'T', 'K', 'S', 'S', 'S', 'A', 'T', 'I', 'E', 'L', 'Y', 'F', 'E'], ['F', 'T', 'L', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', '-', '-', '-', '-', '-', '-', '-', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'C', 'D', 'L', 'T', 'K', '-', 'V', 'K', 'L', 'K', 'Y', 'C', 'G', 'V', 'H', 'F', 'N', 'S', 'Q', 'A', 'I', 'A', 'P', 'T', 'I', 'E', 'Q', 'I', 'D', 'Q', 'S', 'F', 'G', 'A', 'T', 'H', 'P', 'G', 'V', 'Y', 'N', 'S', 'A', 'E', 'Q', '-', '-', '-', '-', 'L', 'F', 'H', 'L', 'N', 'F', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'R', 'G', 'L', 'S', 'F', 'S', 'F', 'Q']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 36.62) self.assertAlmostEqual(alignment.annotations["E-value"], 88) self.assertAlmostEqual(alignment.annotations["Score"], 24.38) self.assertAlmostEqual(alignment.annotations["Identities"], 23) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.342) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 5.900) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEEECCEEecCCCCCCcHHHHHHhhcCCCC ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[87:117], "KLKYCGVHFNSQAIAPTIEQIDQSFGATHP") self.assertEqual(alignment[1], "KLKYCGVHFNSQAIAPTIEQIDQSFGATHP") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~L~Y~~~~~~~~~~~ptf~~I~~~FGPTyP ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~F~~~~~~l~DP~P~~s~e~v~~~~a~~yP ", ) self.assertEqual(alignment.target.id, "H8H183_DEIGI/2") self.assertEqual(alignment.target.seq[4:34], "VFKFDGKVLDDPNPKSTPEQVKTFYAPTYP") self.assertEqual(alignment.target.annotations["hmm_name"], "PF14454.6") self.assertEqual( alignment.target.annotations["hmm_description"], "; Prok_Ub ; Prokaryotic Ubiquitin", ) self.assertEqual(alignment[0], "VFKFDGKVLDDPNPKSTPEQVKTFYAPTYP") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " EEEECCEEecCCCCCCCHHHHHHHHHHhCH ", ) self.assertEqual( str(alignment), """\ H8H183_DE 4 VFKFDGKVLDDPNPKSTPEQVKTFYAPTYP 34 0 ..|..|..........|.||.......|.| 30 sp|Q9BSU1 87 KLKYCGVHFNSQAIAPTIEQIDQSFGATHP 117 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 4, 34], [ 87, 117]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['V', 'F', 'K', 'F', 'D', 'G', 'K', 'V', 'L', 'D', 'D', 'P', 'N', 'P', 'K', 'S', 'T', 'P', 'E', 'Q', 'V', 'K', 'T', 'F', 'Y', 'A', 'P', 'T', 'Y', 'P'], ['K', 'L', 'K', 'Y', 'C', 'G', 'V', 'H', 'F', 'N', 'S', 'Q', 'A', 'I', 'A', 'P', 'T', 'I', 'E', 'Q', 'I', 'D', 'Q', 'S', 'F', 'G', 'A', 'T', 'H', 'P']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 36.36) self.assertAlmostEqual(alignment.annotations["E-value"], 43) self.assertAlmostEqual(alignment.annotations["Score"], 30.67) self.assertAlmostEqual(alignment.annotations["Identities"], 30) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.464) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.500) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " I~~Gmt~~eV~~~lG~p~~~ ", ) self.assertEqual(alignment.target.id, "3N4I_B") self.assertEqual(alignment.target.seq[11:31], "IQFGMTRQQVLDIAGAENCE") self.assertEqual(alignment.target.annotations["hmm_name"], "3N4I_B") self.assertEqual( alignment.target.annotations["hmm_description"], "Crystal structure of the SHV-1; beta-lactamase, protein-protein complex, BLIP, SHV-1; 1.56A {Klebsiella pneumoniae} SCOP: d.98.1.1; Related PDB entries: 3E2K_D 1XXM_C 2G2W_B 3E2L_C 3GMU_B 1XXM_D 3C4P_B 1S0W_C 3C7U_D 3C4O_B 1JTG_B 3C7V_B 3C7V_D 3E2L_D 3E2K_C 2G2U_B 3C7U_B 2B5R_C 1JTG_D 2B5R_D 1S0W_D", ) self.assertEqual(alignment[0], "IQFGMTRQQVLDIAGAENCE") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " SCTTCCHHHHHHHHCGGGEE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHHCCCCee ", ) self.assertEqual( str(alignment), """\ 3N4I_B 11 IQFGMTRQQVLDIAGAENCE 31 0 ..||...|.||...|..... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 11, 31], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'Q', 'F', 'G', 'M', 'T', 'R', 'Q', 'Q', 'V', 'L', 'D', 'I', 'A', 'G', 'A', 'E', 'N', 'C', 'E'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 34.69) self.assertAlmostEqual(alignment.annotations["E-value"], 44) self.assertAlmostEqual(alignment.annotations["Score"], 29.77) self.assertAlmostEqual(alignment.annotations["Identities"], 10) self.assertAlmostEqual(alignment.annotations["Similarity"], -0.059) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.400) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~~Gmt~~~V~~~lG~p~~~ ", ) self.assertEqual(alignment.target.id, "3GMX_B") self.assertEqual(alignment.target.seq[84:104], "TQTGMTEAQFWAAVPSDTCS") self.assertEqual(alignment.target.annotations["hmm_name"], "3GMX_B") self.assertEqual( alignment.target.annotations["hmm_description"], "BLP; 2-layer alpha/beta sandwich, PROTEIN BINDING; HET: ACT; 1.05A {Streptomyces clavuligerus} SCOP: d.98.1.0; Related PDB entries: 3GMX_A 3GMY_A 3GMY_B", ) self.assertEqual(alignment[0], "TQTGMTEAQFWAAVPSDTCS") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCTTCBHHHHHHHSCGGGCE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCCCCCHHHHHHHcCCccce ", ) self.assertEqual( str(alignment), """\ 3GMX_B 84 TQTGMTEAQFWAAVPSDTCS 104 0 ...|...........|.... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 84, 104], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'Q', 'T', 'G', 'M', 'T', 'E', 'A', 'Q', 'F', 'W', 'A', 'A', 'V', 'P', 'S', 'D', 'T', 'C', 'S'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 34.59) self.assertAlmostEqual(alignment.annotations["E-value"], 71) self.assertAlmostEqual(alignment.annotations["Score"], 28.22) self.assertAlmostEqual(alignment.annotations["Identities"], 12) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.088) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.400) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEEEEeccccccccCCCCCcCCCCcCCccchhhHhhccceeecCCCCEEEEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[238:307], "VYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKF", ) self.assertEqual( alignment[1], "VYFGDS-CQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKF", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~f~K~ddrm~IH~~~~~~~~~~~~~dyF~NYF~lG~DiLfd~~t~~v~Ki ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~lG~s~~~~V~~~~G~P~~~~~~~~~~g~~~~Y~~~~~~f~~~~~~~v~~i ", ) self.assertEqual(alignment.target.id, "R4K5N0_CLOPA/8") self.assertEqual( alignment.target.seq[17:69], "FPAKDTNIDSVESKWGKADNSEWVASAKGLYSTYSKHNIVFGSNKGGQIFEV", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF14172.6") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF4309 ; Domain of unknown function (DUF4309)", ) self.assertEqual( alignment[0], "FPAKDTNIDSVESKWGKADNSEWVASAK-----------------GLYSTYSKHNIVFGSNK-GGQIFEV", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCcHHHHHHHhCCCCceehhhhcCceeEEecCceEEEEECCCCeEEEE ", ) self.assertEqual( str(alignment), """\ R4K5N0_CL 17 FPAKDTNIDSVESKWGKADNSEWVASAK-----------------GLYSTYSKHNIVFGS 0 ....|.-...|.|..|...........|-----------------.....|......... sp|Q9BSU1 238 VYFGDS-CQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILF R4K5N0_CL 60 NK-GGQIFEV 69 60 ..-....... 70 sp|Q9BSU1 297 DANTHKVKKF 307 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 17, 23, 24, 45, 45, 62, 62, 69], [238, 244, 244, 265, 282, 299, 300, 307]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['F', 'P', 'A', 'K', 'D', 'T', 'N', 'I', 'D', 'S', 'V', 'E', 'S', 'K', 'W', 'G', 'K', 'A', 'D', 'N', 'S', 'E', 'W', 'V', 'A', 'S', 'A', 'K', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'L', 'Y', 'S', 'T', 'Y', 'S', 'K', 'H', 'N', 'I', 'V', 'F', 'G', 'S', 'N', 'K', '-', 'G', 'G', 'Q', 'I', 'F', 'E', 'V'], ['V', 'Y', 'F', 'G', 'D', 'S', '-', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F', 'Y', 'K', 'S', 'E', 'D', 'K', 'M', 'K', 'I', 'H', 'S', 'P', 'S', 'P', 'H', 'K', 'Q', 'V', 'P', 'S', 'K', 'C', 'N', 'D', 'Y', 'F', 'F', 'N', 'Y', 'F', 'T', 'L', 'G', 'V', 'D', 'I', 'L', 'F', 'D', 'A', 'N', 'T', 'H', 'K', 'V', 'K', 'K', 'F']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 34.21) self.assertAlmostEqual(alignment.annotations["E-value"], 54) self.assertAlmostEqual(alignment.annotations["Score"], 29.27) self.assertAlmostEqual(alignment.annotations["Identities"], 30) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.610) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~~G~t~~eV~~~lG~p~~~ ", ) self.assertEqual(alignment.target.id, "Q8DTX1_STRMU/4") self.assertEqual(alignment.target.seq[94:114], "LKIGESYKKVVEKLGEPDVL") self.assertEqual(alignment.target.annotations["hmm_name"], "PF12978.7") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF3862 ; Domain of Unknown Function with PDB structure (DUF3862)", ) self.assertEqual(alignment[0], "LKIGESYKKVVEKLGEPDVL") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCCCCCHHHHHHHHCCCCee ", ) self.assertEqual( str(alignment), """\ Q8DTX1_ST 94 LKIGESYKKVVEKLGEPDVL 114 0 ...|.|...|...||.|... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 94, 114], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'K', 'I', 'G', 'E', 'S', 'Y', 'K', 'K', 'V', 'V', 'E', 'K', 'L', 'G', 'E', 'P', 'D', 'V', 'L'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 30.93) self.assertAlmostEqual(alignment.annotations["E-value"], 61) self.assertAlmostEqual(alignment.annotations["Score"], 33.05) self.assertAlmostEqual(alignment.annotations["Identities"], 19) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.498) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.000) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:259], "VYFGDSCQDVLSMLGSPHKVF") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKVF") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~f ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~iG~s~~~v~~~~G~P~r~~ ", ) self.assertEqual(alignment.target.id, "4H0A_A") self.assertEqual(alignment.target.seq[42:63], "TWVGKDIKVLTSKFGQADRVY") self.assertEqual(alignment.target.annotations["hmm_name"], "4H0A_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Uncharacterized protein; CAP protein family, cysteine-rich secretory; HET: EDO, MSE; 1.9A {Staphylococcus aureus subsp. aureus}; Related PDB entries: 4H0A_B", ) self.assertEqual(alignment[0], "TWVGKDIKVLTSKFGQADRVY") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " GGTTSBTHHHHHHHCSCSEEE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " HhcCCcHHHHHHHhCCCcEEE ", ) self.assertEqual( str(alignment), """\ 4H0A_A 42 TWVGKDIKVLTSKFGQADRVY 63 0 ...|.......|..|....|. 21 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKVF 259 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 42, 63], [238, 259]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'W', 'V', 'G', 'K', 'D', 'I', 'K', 'V', 'L', 'T', 'S', 'K', 'F', 'G', 'Q', 'A', 'D', 'R', 'V', 'Y'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 30.07) self.assertAlmostEqual(alignment.annotations["E-value"], 3.4e02) self.assertAlmostEqual(alignment.annotations["Score"], 25.76) self.assertAlmostEqual(alignment.annotations["Identities"], 20) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.191) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 6.200) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CCCCccEEcCCcHHHHHHHHHHccCCcCcEEEEECCCCCcCCCEEEEeCCCCeEEEecCcc ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[12:73], "GNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFN", ) self.assertEqual( alignment[1], "GNEQWEFTLGMPLAQAVAILQKHCRII--KNVQVLYSEQ----SPLSHDLILNLTQDGIKLMFDAFN", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " G~~~~~f~LG~sL~~vi~~Lr~~~~~~~~vel~Ys~~~pl~~~Ivi~L~~~GirL~Fd~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " G~EHiEfVi~~~~~~~~~~~~~~~~~~~~~~i~~k~s~~~~~~~r~~NP~~~~~~~~~~VKfH~~s ", ) self.assertEqual(alignment.target.id, "Q7N560_PHOLL/9") self.assertEqual( alignment.target.seq[101:167], "GWEHVELVLPVAPEILSTAAKALLPQPLPAGFSVKESQPKGEQERLPNPTLAITDGEITVKFHPFT", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF06185.12") self.assertEqual( alignment.target.annotations["hmm_description"], "; YecM ; YecM protein" ) self.assertEqual( alignment[0], "GWEHVELVLPVAPEILSTAAKALLPQPLPAGFSVKESQPKGEQERLPNPT-LAITDGEITVKFHPFT", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ceeEEEEEcCCCHHHHHHHHHHhCcCcCCCCCeeEecCCCCccccCCCceEEeecCCEEEEEccCC ", ) self.assertEqual( str(alignment), """\ Q7N560_PH 101 GWEHVELVLPVAPEILSTAAKALLPQPLPAGFSVKESQPKGEQERLPNPT-LAITDGEIT 0 |.|..|..|..................--....|..|..----..|....-|..|...|. sp|Q9BSU1 12 GNEQWEFTLGMPLAQAVAILQKHCRII--KNVQVLYSEQ----SPLSHDLILNLTQDGIK Q7N560_PH 160 VKFHPFT 167 60 ..|..|. 67 sp|Q9BSU1 66 LMFDAFN 73 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[101, 128, 130, 140, 144, 151, 151, 167], [ 12, 39, 39, 49, 49, 56, 57, 73]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'W', 'E', 'H', 'V', 'E', 'L', 'V', 'L', 'P', 'V', 'A', 'P', 'E', 'I', 'L', 'S', 'T', 'A', 'A', 'K', 'A', 'L', 'L', 'P', 'Q', 'P', 'L', 'P', 'A', 'G', 'F', 'S', 'V', 'K', 'E', 'S', 'Q', 'P', 'K', 'G', 'E', 'Q', 'E', 'R', 'L', 'P', 'N', 'P', 'T', '-', 'L', 'A', 'I', 'T', 'D', 'G', 'E', 'I', 'T', 'V', 'K', 'F', 'H', 'P', 'F', 'T'], ['G', 'N', 'E', 'Q', 'W', 'E', 'F', 'T', 'L', 'G', 'M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', '-', '-', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', '-', '-', '-', '-', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 29.78) self.assertAlmostEqual(alignment.annotations["E-value"], 6.8e02) self.assertAlmostEqual(alignment.annotations["Score"], 22.72) self.assertAlmostEqual(alignment.annotations["Identities"], 21) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.270) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 1.300) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " ccccccCCCCccEEcCCcHHHHHHHHHHccCCcCcEEEEECCCCCcCCCEEEEeCCCCeEEEecCccceeeEEEEecCCCCEEEECCEEecCCCCCCcHHHHHHhhcCCCCCCccCcccEEEEEeCcEEEEeeCcccCCCCccCCCcccccccCCCCCCCeEEEEEEEe ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[6:175], "VPERSLGNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKRMYIYS", ) self.assertEqual( alignment[1], "VPERSLGNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAE----------------QLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKRMYIYS", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~Pg~~LG~~~~~f~LG~sL~~vi~~Lr~~~~~~~~vel~Ys~~~pl~~~Ivi~L~~~GirL~Fd~~~QrL~lIEv~d~~~~~L~Y~~~~~~~~~~~ptf~~I~~~FGPTyPG~yd~~~~~Y~LsYpGisF~Fpi~~~~~~~~~~~~~~~~l~~l~~~~~~~~s~i~If~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ipgegtgI~Ls~GQiLkf~N~PlaEI~~~Ydpsn~S~vSS~VklKGtIHPLFEvPsqisien~Q~nEN~LI~sgfgtslpq~y~~pangyl~~~itnt~tgnigqitl~~g~~tmtfnlqtgenkipviagtqit~~~lts~sailiye ", ) self.assertEqual(alignment.target.id, "4IL7_A") self.assertEqual( alignment.target.seq[8:157], "IPGEGTGIQLSAGQILKFYNVPIAEIIVEYDPSNVSGVSSNVKLKGTIHPLFEVPSQISIENFQPTENYLIYSGFGTSLPQTYTIPANGYLIISITNTSTGNIGQITLTIGSTTMTFNLQTGENKIPVIAGTQITNMTLTSSSAILIYE", ) self.assertEqual(alignment.target.annotations["hmm_name"], "4IL7_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Putative uncharacterized protein; partial jelly roll fold, hypothetical; 1.4A {Sulfolobus turreted icosahedral virus}", ) self.assertEqual( alignment[0], "IPGEGTG-----IQLSAG-----QILKFYNVPIAEIIVEYDPSNVSGVSSNVKLK-GTIHPLFEVPSQ--ISIENFQPTENYLIYSG------------------FGTSLPQTYTIPANGYLIISITNTSTGNIGQITLTIGSTTMTFNLQTGENKIPVIAGTQITNMTL-----TSSSAILIYE", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CEEEEEEEEEEECSSCEECCSSEEEEEEEECSSCSEEEEEEEEETTEEEEEEEESEEEEEEECTTCEEEEEEEEEEEEEEEEE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCcceEeccccEEEEecccHheEEEEeCCCCcCCccceeEeeeeeeeceecceeeeeeccCCCCcEEEEecCCCCCCceEEEcCCcEEEEEEEeCCCCceeEEEEEEeeEEEEEEeccCCccccEEeeceeEeeeecCcceEeeee ", ) self.assertEqual( str(alignment), """\ 4IL7_A 8 IPGEGTG-----IQLSAG-----QILKFYNVPIAEIIVEYDPSNVSGVSSNVKLK-GTIH 0 .|....|-----..|...-----.||......|....|.|.............|.-..|. sp|Q9BSU1 6 VPERSLGNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIK 4IL7_A 57 PLFEVPSQ--ISIENFQPTENYLIYSG------------------FGTSLPQTYTIPANG 60 ..|....|--..||....|...|.|.|------------------||...|..|....-- sp|Q9BSU1 66 LMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAE-- 4IL7_A 97 YLIISITNTSTGNIGQITLTIGSTTMTFNLQTGENKIPVIAGTQITNMTL-----TSSSA 120 --------------....|........|.|...................|-----..... sp|Q9BSU1 124 --------------QLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKR 4IL7_A 152 ILIYE 157 180 ..||. 185 sp|Q9BSU1 170 MYIYS 175 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 8, 15, 15, 21, 21, 53, 53, 65, 65, 82, 82, 95, 111, 147, 147, 157], [ 6, 13, 18, 24, 29, 61, 62, 74, 76, 93, 111, 124, 124, 160, 165, 175]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'P', 'G', 'E', 'G', 'T', 'G', '-', '-', '-', '-', '-', 'I', 'Q', 'L', 'S', 'A', 'G', '-', '-', '-', '-', '-', 'Q', 'I', 'L', 'K', 'F', 'Y', 'N', 'V', 'P', 'I', 'A', 'E', 'I', 'I', 'V', 'E', 'Y', 'D', 'P', 'S', 'N', 'V', 'S', 'G', 'V', 'S', 'S', 'N', 'V', 'K', 'L', 'K', '-', 'G', 'T', 'I', 'H', 'P', 'L', 'F', 'E', 'V', 'P', 'S', 'Q', '-', '-', 'I', 'S', 'I', 'E', 'N', 'F', 'Q', 'P', 'T', 'E', 'N', 'Y', 'L', 'I', 'Y', 'S', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'F', 'G', 'T', 'S', 'L', 'P', 'Q', 'T', 'Y', 'T', 'I', 'P', 'A', 'N', 'G', 'Y', 'L', 'I', 'I', 'S', 'I', 'T', 'N', 'T', 'S', 'T', 'G', 'N', 'I', 'G', 'Q', 'I', 'T', 'L', 'T', 'I', 'G', 'S', 'T', 'T', 'M', 'T', 'F', 'N', 'L', 'Q', 'T', 'G', 'E', 'N', 'K', 'I', 'P', 'V', 'I', 'A', 'G', 'T', 'Q', 'I', 'T', 'N', 'M', 'T', 'L', '-', '-', '-', '-', '-', 'T', 'S', 'S', 'S', 'A', 'I', 'L', 'I', 'Y', 'E'], ['V', 'P', 'E', 'R', 'S', 'L', 'G', 'N', 'E', 'Q', 'W', 'E', 'F', 'T', 'L', 'G', 'M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'C', 'D', 'L', 'T', 'K', 'V', 'K', 'L', 'K', 'Y', 'C', 'G', 'V', 'H', 'F', 'N', 'S', 'Q', 'A', 'I', 'A', 'P', 'T', 'I', 'E', 'Q', 'I', 'D', 'Q', 'S', 'F', 'G', 'A', 'T', 'H', 'P', 'G', 'V', 'Y', 'N', 'S', 'A', 'E', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'Q', 'L', 'F', 'H', 'L', 'N', 'F', 'R', 'G', 'L', 'S', 'F', 'S', 'F', 'Q', 'L', 'D', 'S', 'W', 'T', 'E', 'A', 'P', 'K', 'Y', 'E', 'P', 'N', 'F', 'A', 'H', 'G', 'L', 'A', 'S', 'L', 'Q', 'I', 'P', 'H', 'G', 'A', 'T', 'V', 'K', 'R', 'M', 'Y', 'I', 'Y', 'S']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 26.30) self.assertAlmostEqual(alignment.annotations["E-value"], 89) self.assertAlmostEqual(alignment.annotations["Score"], 29.01) self.assertAlmostEqual(alignment.annotations["Identities"], 25) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.605) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.500) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " I~~Gmt~~eV~~~lG~p~~~ ", ) self.assertEqual(alignment.target.id, "3D4E_A") self.assertEqual(alignment.target.seq[113:133], "LKIGESYKKIVEKLGEPDVL") self.assertEqual(alignment.target.annotations["hmm_name"], "3D4E_A") self.assertEqual( alignment.target.annotations["hmm_description"], "putative beta-lactamase inhibitor protein; NP_721579.1, putative beta-lactamase inhibitor protein; HET: EDO, MSE; 1.4A {Streptococcus mutans}", ) self.assertEqual(alignment[0], "LKIGESYKKIVEKLGEPDVL") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCTTCBHHHHHHHHCCCSEE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHHCCCcee ", ) self.assertEqual( str(alignment), """\ 3D4E_A 113 LKIGESYKKIVEKLGEPDVL 133 0 ...|.|.......||.|... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[113, 133], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'K', 'I', 'G', 'E', 'S', 'Y', 'K', 'K', 'I', 'V', 'E', 'K', 'L', 'G', 'E', 'P', 'D', 'V', 'L'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 24.37) self.assertAlmostEqual(alignment.annotations["E-value"], 1.1e02) self.assertAlmostEqual(alignment.annotations["Score"], 28.12) self.assertAlmostEqual(alignment.annotations["Identities"], 25) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.287) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.500) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~~Gmt~~eV~~~lG~p~~~ ", ) self.assertEqual(alignment.target.id, "3N4I_B") self.assertEqual(alignment.target.seq[90:110], "VTVGMTRAQVLATVGQGSCT") self.assertEqual(alignment.target.annotations["hmm_name"], "3N4I_B") self.assertEqual( alignment.target.annotations["hmm_description"], "Crystal structure of the SHV-1; beta-lactamase, protein-protein complex, BLIP, SHV-1; 1.56A {Klebsiella pneumoniae} SCOP: d.98.1.1; Related PDB entries: 3E2K_D 1XXM_C 2G2W_B 3E2L_C 3GMU_B 1XXM_D 3C4P_B 1S0W_C 3C7U_D 3C4O_B 1JTG_B 3C7V_B 3C7V_D 3E2L_D 3E2K_C 2G2U_B 3C7U_B 2B5R_C 1JTG_D 2B5R_D 1S0W_D", ) self.assertEqual(alignment[0], "VTVGMTRAQVLATVGQGSCT") self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CCTTCBHHHHHHHHCTBSEE ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ccCCCCHHHHHHHHCCCcee ", ) self.assertEqual( str(alignment), """\ 3N4I_B 90 VTVGMTRAQVLATVGQGSCT 110 0 |..|.....||...|..... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 90, 110], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['V', 'T', 'V', 'G', 'M', 'T', 'R', 'A', 'Q', 'V', 'L', 'A', 'T', 'V', 'G', 'Q', 'G', 'S', 'C', 'T'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 23.84) self.assertAlmostEqual(alignment.annotations["E-value"], 89) self.assertAlmostEqual(alignment.annotations["Score"], 26.82) self.assertAlmostEqual(alignment.annotations["Identities"], 10) self.assertAlmostEqual(alignment.annotations["Similarity"], -0.092) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.800) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEecCCHHHHHHHhcCCcEEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:259], "VYFGDSCQDVLSMLGSPHKVF") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKVF") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~~G~T~QDVl~~LG~P~~~f ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~~G~t~~~V~~~lG~p~~~~ ", ) self.assertEqual(alignment.target.id, "B5GLC0_STRC2/3") self.assertEqual(alignment.target.seq[80:101], "TQTGMTEAQFWAAVPSDTCSA") self.assertEqual(alignment.target.annotations["hmm_name"], "PF07467.11") self.assertEqual( alignment.target.annotations["hmm_description"], "; BLIP ; Beta-lactamase inhibitor (BLIP)", ) self.assertEqual(alignment[0], "TQTGMTEAQFWAAVPSDTCSA") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCCCCCHHHHHHhcCCccccc ", ) self.assertEqual( str(alignment), """\ B5GLC0_ST 80 TQTGMTEAQFWAAVPSDTCSA 101 0 ...|...........|..... 21 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKVF 259 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 80, 101], [238, 259]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'Q', 'T', 'G', 'M', 'T', 'E', 'A', 'Q', 'F', 'W', 'A', 'A', 'V', 'P', 'S', 'D', 'T', 'C', 'S', 'A'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 21.56) self.assertAlmostEqual(alignment.annotations["E-value"], 3.9e02) self.assertAlmostEqual(alignment.annotations["Score"], 22.84) self.assertAlmostEqual(alignment.annotations["Identities"], 13) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.078) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.800) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEcCCcHHHHHHHHHHccCCcCcEEEEECCCCCcCCCEEEEeCCCCeEEEecCccceeeEEEEecCCCCEEEECCEEecCCCCCCcHHHHHHhhcC ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[18:114], "FTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGA", ) self.assertEqual( alignment[1], "FTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVH-FNSQAIAPTIEQIDQSFGA", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " f~LG~sL~~vi~~Lr~~~~~~~~vel~Ys~~~pl~~~Ivi~L~~~GirL~Fd~~~QrL~lIEv~d~~~~~L~Y~~~~~~~~~~~ptf~~I~~~FGP ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " I~~G~t~~~V~~~lG~P~~~~~~~~~~~~y~~~~~~~~~~~v~F~~~gkv~~k~~~~~~~~~~~~~t~~~~~~i~~G~t~~~V~~~lG~ ", ) self.assertEqual(alignment.target.id, "B5GLC0_STRC2/3") self.assertEqual( alignment.target.seq[7:96], "IQFGMDRTLVWQLAGADQSCSDQVERIICYNNPDHYGPQGHFFFNAADKLIHKRQMELFPAPKPTMRLATYNKTQTGMTEAQFWAAVPS", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF07467.11") self.assertEqual( alignment.target.annotations["hmm_description"], "; BLIP ; Beta-lactamase inhibitor (BLIP)", ) self.assertEqual( alignment[0], "IQFGMDRTLVWQLAGADQSCSDQVERIICYNNPDH-------YGPQGHFFFNA-ADKLIHKRQMELFPAPKPTMRLATYNKTQTGMTEAQFWAAVPS", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHHCCCceecCCcceEEEEeCCCCCCCEEEEEEcCCCEEEEEEECCCCCCCCCCCCHHHHHhcCCCCCHHHHHHhcCC ", ) self.assertEqual( str(alignment), """\ B5GLC0_ST 7 IQFGMDRTLVWQLAGADQSCSDQVERIICYNNPDH-------YGPQGHFFFNA-ADKLIH 0 ...||..................|........|..-------........|.|-...|.. sp|Q9BSU1 18 FTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKV B5GLC0_ST 59 KRQMELFPAPKPTMRLATYNKTQTGMTEAQFWAAVPS 96 60 .....|...........-.|......|..|....... 97 sp|Q9BSU1 78 IEVCDLTKVKLKYCGVH-FNSQAIAPTIEQIDQSFGA 114 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 7, 42, 42, 53, 53, 76, 77, 96], [ 18, 53, 60, 71, 72, 95, 95, 114]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'Q', 'F', 'G', 'M', 'D', 'R', 'T', 'L', 'V', 'W', 'Q', 'L', 'A', 'G', 'A', 'D', 'Q', 'S', 'C', 'S', 'D', 'Q', 'V', 'E', 'R', 'I', 'I', 'C', 'Y', 'N', 'N', 'P', 'D', 'H', '-', '-', '-', '-', '-', '-', '-', 'Y', 'G', 'P', 'Q', 'G', 'H', 'F', 'F', 'F', 'N', 'A', '-', 'A', 'D', 'K', 'L', 'I', 'H', 'K', 'R', 'Q', 'M', 'E', 'L', 'F', 'P', 'A', 'P', 'K', 'P', 'T', 'M', 'R', 'L', 'A', 'T', 'Y', 'N', 'K', 'T', 'Q', 'T', 'G', 'M', 'T', 'E', 'A', 'Q', 'F', 'W', 'A', 'A', 'V', 'P', 'S'], ['F', 'T', 'L', 'G', 'M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'C', 'D', 'L', 'T', 'K', 'V', 'K', 'L', 'K', 'Y', 'C', 'G', 'V', 'H', '-', 'F', 'N', 'S', 'Q', 'A', 'I', 'A', 'P', 'T', 'I', 'E', 'Q', 'I', 'D', 'Q', 'S', 'F', 'G', 'A']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_length(self): """Test getting the number of alignments without parsing the file.""" stream = open(self.path) alignments = Align.parse(stream, "hhr") stream.close() self.assertEqual(len(alignments), 34) class Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30(unittest.TestCase): path = os.path.join("HHsuite", "hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr") def test_reading(self): alignments = Align.parse(self.path, "hhr") self.assertEqual(alignments.metadata["No_of_seqs"], (149, 573)) self.assertAlmostEqual(alignments.metadata["Neff"], 6.62119) self.assertEqual(alignments.metadata["Searched_HMMs"], 16712) self.assertEqual(alignments.metadata["Rundate"], "Wed Feb 13 09:26:07 2019") self.assertEqual( alignments.metadata["Command line"], "/home/shah/hh-suite/build/bin/hhsearch -i /home/shah/seq/q9bsu1/hhblits/q9bsu1_uniclust_w_ss.a3m -d /home/shah/db/pfamA_30/pfam -o /home/shah/seq/q9bsu1/hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr -p 20 -Z 250 -loc -z 1 -b 1 -B 250 -ssm 2 -sc 1 -seq 1 -dbstrlen 10000 -norealign -maxres 32000", ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 2e-106, places=107) self.assertAlmostEqual(alignment.annotations["Score"], 822.75) self.assertAlmostEqual(alignment.annotations["Identities"], 88) self.assertAlmostEqual(alignment.annotations["Similarity"], 1.401) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 6.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " ccCCCCceEEcCCcHHHHHHHHHHccCccccEEEEECCCCCcCCCeEEEecCCCeEEEeccccCceeEEEEecCCCCEEEECCEEecCCCCCCcHhHHHhhcCCCCCCCccCccceEEeeeCeEEEEeeCcccCCCCccCCCcccccccCCCCCCCeEEEEEEEeCCChHhcCCCCCCcchhcCcceeEEEEEeeCCCCCceEEEEEEecCCCCccccccceeEEEEEEEeCCchHHHHHhhcCCcEEEEcCcccCccCCCCCCcCCCCcccccchhHHHhccceeecCCCCeEEEEEecCCCCCCchhhcccCCcEEeeccccccCCCCCcccccCCCCHHHHHHHhCCCCCCCeEeeCCCCCCCCCCCCceEEeccCCEEEEEecCCCEEEEEEe ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[10:407], "SLGNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKRMYIYSGNSLQDTKAPMMPLSCFLGNVYAESVDVLRDGTGPAGLRLRLLAAGCGPGLLADAKMRVFERSVYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTNYPGHYNFNIYHRCEFKIPLAIKKENADGQTETCTTYSKWDNIQELLGHPVEKPVVLHRSSSPNNTNPFGSTFCFGLQRMIFEVMQNNHIASVTLY", ) self.assertEqual( alignment[1], "SLGNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKRMYIYSGNSLQDTKAPMMPLSCFLGNVYAESVDVLRDGTGPAGLRLRLLAAGCGPGLLADAKMRVFERSVYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTNYPGHYNFNIYHRCEFKIPLAIKKENADGQTE--TCTTYSKWDNIQELLGHPVEKPVVLHRSSSPNNTNPFGSTFCFGLQRMIFEVMQNNHIASVTLY", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~LG~~~~~f~LG~sL~~vi~~Lr~~~~~~~~Vel~Ys~~~Pl~~dIvi~L~~~GirL~Fd~~~QrL~lIEV~d~s~v~L~Y~g~~~~~~~~~pT~~~I~~~FGPTyPG~yd~~~~~Y~LsYpGisF~Fpi~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~m~If~G~s~~~~~~~~~p~~~~~~~~~~~~v~v~~~~~~~~gl~~~~~~~~~~~~~~~~~~~~~~~~~I~fG~T~QDVl~~LG~P~~vf~K~ddrm~IH~~~~~~~~~~~~~dyF~NYF~lGlDiLfd~~th~v~KiILHtN~PGh~~F~~Y~RC~f~i~~~~~~~~~~~~~~~it~~~k~~~i~~~l~~~~~~pvvlnR~~s~~~~npfg~T~lyG~~~~ifEVm~n~~IasVTlf ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "~lG~f~LG~sL~~vl~~Lr~~~~~~~~v~i~Ys~~~P~~~~Ivi~Lp~~GirL~Fd~~~QrL~lIEv~d~~~~~L~Y~~~~~~~~~~~~tf~~Iy~~FGPTyPG~~d~~~~~y~LsYpGlsF~Fp~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~If~G~~~~~~~~p~~p~~~~~~~~~~~~v~v~~~~~~~~g~~l~f~~~~~~~~~~~~~~~~~~~~~I~~G~TtQDVl~~LG~P~~vf~K~ddrm~IH~~~~~~~~~~~~~~yF~NYF~lGlDiLfd~~th~v~KiILHtN~Pg~~~F~~Y~RC~w~i~~~~~~~~~~~~~~~~~i~~~~~~~~i~~~l~~~~~~p~vLnR~~~~~~~~~~g~t~lyG~~g~IfEV~~ng~IasVTlf", ) self.assertEqual(alignment.target.id, "Q1LV04_DANRE/1") self.assertEqual( alignment.target.seq[0:395], "EQWEFALGMPLAQAISILQKHCRIIKNVQVLYSEQMPLSHDLILNLTQDGIKLLFDACNQRLKVIEVYDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNAAEQLFHLNFRGLSFSFQLDSWSEAPKYEPNFAHGLASLQIPHGATVKRMYIYSGNNLQETKAPAMPLACFLGNVYAECVEVLRDGAGPLGLKLRLLTAGCGPGVLADTKVRAVERSIYFGDSCQDVLSALGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYYILGVDILFDSTTHLVKKFVLHTNFPGHYNFNIYHRCDFKIPLIIKKDGADAHSEDCILTTYSKWDQIQELLGHPMEKPVVLHRSSSANNTNPFGSTFCFGLQRMIFEVMQNNHIASVTLY", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF03676.13") self.assertEqual( alignment.target.annotations["hmm_description"], "; UPF0183 ; Uncharacterised protein family (UPF0183)", ) self.assertEqual( alignment[0], "EQWE----FALGMPLAQAISILQKHCRIIKNVQVLYSEQMPLSHDLILNLTQDGIKLLFDACNQRLKVIEVYDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNAAEQLFHLNFRGLSFSFQLDSWSEAPKYEPNFAHGLASLQIPHGATVKRMYIYSGNNLQETKAPAMPLACFLGNVYAECVEVLRDGAGPLGLKLRLLTAGCGPGVLADTKVRAVERSIYFGDSCQDVLSALGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYYILGVDILFDSTTHLVKKFVLHTNFPGHYNFNIYHRCDFKIPLIIKKDGADAHSEDCILTTYSKWDQIQELLGHPMEKPVVLHRSSSANNTNPFGSTFCFGLQRMIFEVMQNNHIASVTLY", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCccEEeCCcHHHHHHHHHhcccccccEEEEECCCCccCCcEEEEeCCCcEEEEEcCCCcEEEEEEEEcCCccEEEECCEEecCCCCCCCHHHHHHHhcCCCCCccccccCEEEEeeCCEEEEeeCCccccCCccCCCcccccccccCCCCCeeEEEEEeeCCCccccCCCCCCchhcCCceeeEEEEEEeCCCCCcceEEEEEeCCCCCCcccccccccceEEEEecCCHHHHHHHhCCCceEEEcCcccccccCCCCCCCCCccccccchhhHHhceeeeeeCCCceeEEEEEecCCCCccccCccccCcEEEEecCCcCCCccCcccceecCCCcHHHHHHHhcCCCCCCEEEecCCCCCCCCCCccEEEEeeCCEEEEEecCCcEEEEEeC", ) self.assertEqual( str(alignment), """\ Q1LV04_DA 0 EQWE----FALGMPLAQAISILQKHCRIIKNVQVLYSEQMPLSHDLILNLTQDGIKLLFD 0 ....----|.||||||||..|||||||||||||||||||.|||||||||||||||||.|| sp|Q9BSU1 10 SLGNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFD Q1LV04_DA 56 ACNQRLKVIEVYDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNAAEQLFHLN 60 |.|||||||||.|||||||||||||||||||||||||||||||||||||||.|||||||| sp|Q9BSU1 70 AFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLN Q1LV04_DA 116 FRGLSFSFQLDSWSEAPKYEPNFAHGLASLQIPHGATVKRMYIYSGNNLQETKAPAMPLA 120 |||||||||||||.|||||||||||||||||||||||||||||||||.||.||||.|||. sp|Q9BSU1 130 FRGLSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKRMYIYSGNSLQDTKAPMMPLS Q1LV04_DA 176 CFLGNVYAECVEVLRDGAGPLGLKLRLLTAGCGPGVLADTKVRAVERSIYFGDSCQDVLS 180 |||||||||.|.|||||.||.||.||||.||||||.|||.|.|..|||.||||||||||| sp|Q9BSU1 190 CFLGNVYAESVDVLRDGTGPAGLRLRLLAAGCGPGLLADAKMRVFERSVYFGDSCQDVLS Q1LV04_DA 236 ALGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYYILGVDILFDSTTHLVKKFVLH 240 .|||||||||||||||||||||||||||||||||||||..||||||||..||.||||||| sp|Q9BSU1 250 MLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLH Q1LV04_DA 296 TNFPGHYNFNIYHRCDFKIPLIIKKDGADAHSEDCILTTYSKWDQIQELLGHPMEKPVVL 300 ||.||||||||||||.|||||.|||..||...|--..|||||||.||||||||.|||||| sp|Q9BSU1 310 TNYPGHYNFNIYHRCEFKIPLAIKKENADGQTE--TCTTYSKWDNIQELLGHPVEKPVVL Q1LV04_DA 356 HRSSSANNTNPFGSTFCFGLQRMIFEVMQNNHIASVTLY 395 360 |||||.||||||||||||||||||||||||||||||||| 399 sp|Q9BSU1 368 HRSSSPNNTNPFGSTFCFGLQRMIFEVMQNNHIASVTLY 407 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 4, 4, 329, 331, 395], [ 10, 14, 18, 343, 343, 407]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['E', 'Q', 'W', 'E', '-', '-', '-', '-', 'F', 'A', 'L', 'G', 'M', 'P', 'L', 'A', 'Q', 'A', 'I', 'S', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'M', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'L', 'F', 'D', 'A', 'C', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'Y', 'D', 'L', 'T', 'K', 'V', 'K', 'L', 'K', 'Y', 'C', 'G', 'V', 'H', 'F', 'N', 'S', 'Q', 'A', 'I', 'A', 'P', 'T', 'I', 'E', 'Q', 'I', 'D', 'Q', 'S', 'F', 'G', 'A', 'T', 'H', 'P', 'G', 'V', 'Y', 'N', 'A', 'A', 'E', 'Q', 'L', 'F', 'H', 'L', 'N', 'F', 'R', 'G', 'L', 'S', 'F', 'S', 'F', 'Q', 'L', 'D', 'S', 'W', 'S', 'E', 'A', 'P', 'K', 'Y', 'E', 'P', 'N', 'F', 'A', 'H', 'G', 'L', 'A', 'S', 'L', 'Q', 'I', 'P', 'H', 'G', 'A', 'T', 'V', 'K', 'R', 'M', 'Y', 'I', 'Y', 'S', 'G', 'N', 'N', 'L', 'Q', 'E', 'T', 'K', 'A', 'P', 'A', 'M', 'P', 'L', 'A', 'C', 'F', 'L', 'G', 'N', 'V', 'Y', 'A', 'E', 'C', 'V', 'E', 'V', 'L', 'R', 'D', 'G', 'A', 'G', 'P', 'L', 'G', 'L', 'K', 'L', 'R', 'L', 'L', 'T', 'A', 'G', 'C', 'G', 'P', 'G', 'V', 'L', 'A', 'D', 'T', 'K', 'V', 'R', 'A', 'V', 'E', 'R', 'S', 'I', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'A', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F', 'Y', 'K', 'S', 'E', 'D', 'K', 'M', 'K', 'I', 'H', 'S', 'P', 'S', 'P', 'H', 'K', 'Q', 'V', 'P', 'S', 'K', 'C', 'N', 'D', 'Y', 'F', 'F', 'N', 'Y', 'Y', 'I', 'L', 'G', 'V', 'D', 'I', 'L', 'F', 'D', 'S', 'T', 'T', 'H', 'L', 'V', 'K', 'K', 'F', 'V', 'L', 'H', 'T', 'N', 'F', 'P', 'G', 'H', 'Y', 'N', 'F', 'N', 'I', 'Y', 'H', 'R', 'C', 'D', 'F', 'K', 'I', 'P', 'L', 'I', 'I', 'K', 'K', 'D', 'G', 'A', 'D', 'A', 'H', 'S', 'E', 'D', 'C', 'I', 'L', 'T', 'T', 'Y', 'S', 'K', 'W', 'D', 'Q', 'I', 'Q', 'E', 'L', 'L', 'G', 'H', 'P', 'M', 'E', 'K', 'P', 'V', 'V', 'L', 'H', 'R', 'S', 'S', 'S', 'A', 'N', 'N', 'T', 'N', 'P', 'F', 'G', 'S', 'T', 'F', 'C', 'F', 'G', 'L', 'Q', 'R', 'M', 'I', 'F', 'E', 'V', 'M', 'Q', 'N', 'N', 'H', 'I', 'A', 'S', 'V', 'T', 'L', 'Y'], ['S', 'L', 'G', 'N', 'E', 'Q', 'W', 'E', 'F', 'T', 'L', 'G', 'M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'C', 'D', 'L', 'T', 'K', 'V', 'K', 'L', 'K', 'Y', 'C', 'G', 'V', 'H', 'F', 'N', 'S', 'Q', 'A', 'I', 'A', 'P', 'T', 'I', 'E', 'Q', 'I', 'D', 'Q', 'S', 'F', 'G', 'A', 'T', 'H', 'P', 'G', 'V', 'Y', 'N', 'S', 'A', 'E', 'Q', 'L', 'F', 'H', 'L', 'N', 'F', 'R', 'G', 'L', 'S', 'F', 'S', 'F', 'Q', 'L', 'D', 'S', 'W', 'T', 'E', 'A', 'P', 'K', 'Y', 'E', 'P', 'N', 'F', 'A', 'H', 'G', 'L', 'A', 'S', 'L', 'Q', 'I', 'P', 'H', 'G', 'A', 'T', 'V', 'K', 'R', 'M', 'Y', 'I', 'Y', 'S', 'G', 'N', 'S', 'L', 'Q', 'D', 'T', 'K', 'A', 'P', 'M', 'M', 'P', 'L', 'S', 'C', 'F', 'L', 'G', 'N', 'V', 'Y', 'A', 'E', 'S', 'V', 'D', 'V', 'L', 'R', 'D', 'G', 'T', 'G', 'P', 'A', 'G', 'L', 'R', 'L', 'R', 'L', 'L', 'A', 'A', 'G', 'C', 'G', 'P', 'G', 'L', 'L', 'A', 'D', 'A', 'K', 'M', 'R', 'V', 'F', 'E', 'R', 'S', 'V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F', 'Y', 'K', 'S', 'E', 'D', 'K', 'M', 'K', 'I', 'H', 'S', 'P', 'S', 'P', 'H', 'K', 'Q', 'V', 'P', 'S', 'K', 'C', 'N', 'D', 'Y', 'F', 'F', 'N', 'Y', 'F', 'T', 'L', 'G', 'V', 'D', 'I', 'L', 'F', 'D', 'A', 'N', 'T', 'H', 'K', 'V', 'K', 'K', 'F', 'V', 'L', 'H', 'T', 'N', 'Y', 'P', 'G', 'H', 'Y', 'N', 'F', 'N', 'I', 'Y', 'H', 'R', 'C', 'E', 'F', 'K', 'I', 'P', 'L', 'A', 'I', 'K', 'K', 'E', 'N', 'A', 'D', 'G', 'Q', 'T', 'E', '-', '-', 'T', 'C', 'T', 'T', 'Y', 'S', 'K', 'W', 'D', 'N', 'I', 'Q', 'E', 'L', 'L', 'G', 'H', 'P', 'V', 'E', 'K', 'P', 'V', 'V', 'L', 'H', 'R', 'S', 'S', 'S', 'P', 'N', 'N', 'T', 'N', 'P', 'F', 'G', 'S', 'T', 'F', 'C', 'F', 'G', 'L', 'Q', 'R', 'M', 'I', 'F', 'E', 'V', 'M', 'Q', 'N', 'N', 'H', 'I', 'A', 'S', 'V', 'T', 'L', 'Y']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 71.64) self.assertAlmostEqual(alignment.annotations["E-value"], 0.97) self.assertAlmostEqual(alignment.annotations["Score"], 31.45) self.assertAlmostEqual(alignment.annotations["Identities"], 30) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.363) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.700) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEeCCchHHHHHhhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~fG~T~QDVl~~LG~P~~v ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~~G~Tk~eV~~~lG~P~~~ ", ) self.assertEqual(alignment.target.id, "A6W2D6_MARMS/3") self.assertEqual(alignment.target.seq[11:31], "LQIGMSESQVTYLLGNPMLR") self.assertEqual(alignment.target.annotations["hmm_name"], "PF04355.12") self.assertEqual( alignment.target.annotations["hmm_description"], "; SmpA_OmlA ; SmpA / OmlA family", ) self.assertEqual(alignment[0], "LQIGMSESQVTYLLGNPMLR") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHHCCCCcc ", ) self.assertEqual( str(alignment), """\ A6W2D6_MA 11 LQIGMSESQVTYLLGNPMLR 31 0 ...|.|...|...||.|... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 11, 31], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'Q', 'I', 'G', 'M', 'S', 'E', 'S', 'Q', 'V', 'T', 'Y', 'L', 'L', 'G', 'N', 'P', 'M', 'L', 'R'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 53.47) self.assertAlmostEqual(alignment.annotations["E-value"], 4.1) self.assertAlmostEqual(alignment.annotations["Score"], 30.99) self.assertAlmostEqual(alignment.annotations["Identities"], 15) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.388) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.100) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEeCCchHHHHHhhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~fG~T~QDVl~~LG~P~~v ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " l~~GMTk~qV~~iLG~P~~~ ", ) self.assertEqual(alignment.target.id, "A3QGB8_SHELP/1") self.assertEqual(alignment.target.seq[33:53], "LSLGMTRDQVMTLMGTADFN") self.assertEqual(alignment.target.annotations["hmm_name"], "PF11399.7") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF3192 ; Protein of unknown function (DUF3192)", ) self.assertEqual(alignment[0], "LSLGMTRDQVMTLMGTADFN") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCHHHHHHHhCCCcee ", ) self.assertEqual( str(alignment), """\ A3QGB8_SH 33 LSLGMTRDQVMTLMGTADFN 53 0 ...|.....|....|..... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 33, 53], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'S', 'L', 'G', 'M', 'T', 'R', 'D', 'Q', 'V', 'M', 'T', 'L', 'M', 'G', 'T', 'A', 'D', 'F', 'N'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 52.40) self.assertAlmostEqual(alignment.annotations["E-value"], 7.5) self.assertAlmostEqual(alignment.annotations["Score"], 31.10) self.assertAlmostEqual(alignment.annotations["Identities"], 12) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.062) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEeCCchHHHHHhhcCCcEEEEcCcccCccCCCCCCcCCCCcccccchhHHHhccceeecCCCCeEEEEEecCCCCC ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[238:315], "VYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTNYPG", ) self.assertEqual( alignment[1], "VYFGDS-CQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTNYPG", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~fG~T~QDVl~~LG~P~~vf~K~ddrm~IH~~~~~~~~~~~~~dyF~NYF~lGlDiLfd~~th~v~KiILHtN~PG ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~ig~s~~~eV~~~~G~P~~~~~~~~~~g~y~~y~~~~~~fg~~~~~~i~~ir~~~~~l~~ ", ) self.assertEqual(alignment.target.id, "R4K5N0_CLOPA/8") self.assertEqual( alignment.target.seq[17:78], "FPAKDTNIDSVESKWGKADNSEWVASAKGLYSTYSKHNIVFGSNKGGQIFEVRSLDKQLGN", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF14172.5") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF4309 ; Domain of unknown function (DUF4309)", ) self.assertEqual( alignment[0], "FPAKDTNIDSVESKWGKADNSEWVASAK-----------------GLYSTYSKHNIVFGSNKGGQIFEVRSLDKQLGN", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCcHHHHHHHhCCCCceehhhhcCCeeEEEeCCeEEEEECCCCcEEEEEEeCccccc ", ) self.assertEqual( str(alignment), """\ R4K5N0_CL 17 FPAKDTNIDSVESKWGKADNSEWVASAK-----------------GLYSTYSKHNIVFGS 0 ....|.-...|.|..|...........|-----------------.....|......... sp|Q9BSU1 238 VYFGDS-CQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILF R4K5N0_CL 60 NKGGQIFEVRSLDKQLGN 78 60 ...........|...... 78 sp|Q9BSU1 297 DANTHKVKKFVLHTNYPG 315 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 17, 23, 24, 45, 45, 78], [238, 244, 244, 265, 282, 315]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['F', 'P', 'A', 'K', 'D', 'T', 'N', 'I', 'D', 'S', 'V', 'E', 'S', 'K', 'W', 'G', 'K', 'A', 'D', 'N', 'S', 'E', 'W', 'V', 'A', 'S', 'A', 'K', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'L', 'Y', 'S', 'T', 'Y', 'S', 'K', 'H', 'N', 'I', 'V', 'F', 'G', 'S', 'N', 'K', 'G', 'G', 'Q', 'I', 'F', 'E', 'V', 'R', 'S', 'L', 'D', 'K', 'Q', 'L', 'G', 'N'], ['V', 'Y', 'F', 'G', 'D', 'S', '-', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F', 'Y', 'K', 'S', 'E', 'D', 'K', 'M', 'K', 'I', 'H', 'S', 'P', 'S', 'P', 'H', 'K', 'Q', 'V', 'P', 'S', 'K', 'C', 'N', 'D', 'Y', 'F', 'F', 'N', 'Y', 'F', 'T', 'L', 'G', 'V', 'D', 'I', 'L', 'F', 'D', 'A', 'N', 'T', 'H', 'K', 'V', 'K', 'K', 'F', 'V', 'L', 'H', 'T', 'N', 'Y', 'P', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 48.79) self.assertAlmostEqual(alignment.annotations["E-value"], 5.3) self.assertAlmostEqual(alignment.annotations["Score"], 29.67) self.assertAlmostEqual(alignment.annotations["Identities"], 27) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.282) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 8.000) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " ccceeEEEEEEEeCCchHHHHHhhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[228:258], "DAKMRVFERSVYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "DAKMRVFERSVYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~~~I~fG~T~QDVl~~LG~P~~v ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "a~s~RCg~~lV~~Gds~~~Vl~~cGeP~~~ ", ) self.assertEqual(alignment.target.id, "H8MKT6_CORCM/2") self.assertEqual(alignment.target.seq[0:30], "ASALRCDNKIVSEGASQVDALAKCGQPVTK") self.assertEqual(alignment.target.annotations["hmm_name"], "PF11006.7") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF2845 ; Protein of unknown function (DUF2845)", ) self.assertEqual(alignment[0], "ASALRCDNKIVSEGASQVDALAKCGQPVTK") self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCCcccCCcccCCCCCHHHHHHHhCCCeee ", ) self.assertEqual( str(alignment), """\ H8MKT6_CO 0 ASALRCDNKIVSEGASQVDALAKCGQPVTK 30 0 ....|.....|..|.|..|.|...|.|... 30 sp|Q9BSU1 228 DAKMRVFERSVYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 30], [228, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'S', 'A', 'L', 'R', 'C', 'D', 'N', 'K', 'I', 'V', 'S', 'E', 'G', 'A', 'S', 'Q', 'V', 'D', 'A', 'L', 'A', 'K', 'C', 'G', 'Q', 'P', 'V', 'T', 'K'], ['D', 'A', 'K', 'M', 'R', 'V', 'F', 'E', 'R', 'S', 'V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 41.13) self.assertAlmostEqual(alignment.annotations["E-value"], 9.7) self.assertAlmostEqual(alignment.annotations["Score"], 29.55) self.assertAlmostEqual(alignment.annotations["Identities"], 26) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.562) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.700) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " eCCchHHHHHhhcCCcEEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[240:259], "FGDSCQDVLSMLGSPHKVF") self.assertEqual(alignment[1], "FGDSCQDVLSMLGSPHKVF") self.assertEqual( alignment.query.letter_annotations["Consensus"], " fG~T~QDVl~~LG~P~~vf ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], "iG~~~~~v~~~lG~P~~~~ ", ) self.assertEqual(alignment.target.id, "U5LAW6_9BACI/1") self.assertEqual(alignment.target.seq[0:19], "IGKNASDLQVLLGDPERKD") self.assertEqual(alignment.target.annotations["hmm_name"], "PF14504.5") self.assertEqual( alignment.target.annotations["hmm_description"], "; CAP_assoc_N ; CAP-associated N-terminal", ) self.assertEqual(alignment[0], "IGKNASDLQVLLGDPERKD") self.assertEqual( alignment.target.letter_annotations["ss_pred"], "CCCCHHHHHHHHCCCceeC ", ) self.assertEqual( str(alignment), """\ U5LAW6_9B 0 IGKNASDLQVLLGDPERKD 19 0 .|....|....||.|.... 19 sp|Q9BSU1 240 FGDSCQDVLSMLGSPHKVF 259 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 19], [240, 259]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'G', 'K', 'N', 'A', 'S', 'D', 'L', 'Q', 'V', 'L', 'L', 'G', 'D', 'P', 'E', 'R', 'K', 'D'], ['F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', 'F']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 41.12) self.assertAlmostEqual(alignment.annotations["E-value"], 17) self.assertAlmostEqual(alignment.annotations["Score"], 28.06) self.assertAlmostEqual(alignment.annotations["Identities"], 7) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.077) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.700) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEeCCchHHHHHhhcCCcEEEEcCcccCccCCCCCCcCCCCcccccchhHHHhccceeecCCCCeEEEEEe ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[238:309], "VYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVL", ) self.assertEqual( alignment[1], "VYFGDSCQDVLSMLGSPHKV---------FYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVL", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~fG~T~QDVl~~LG~P~~vf~K~ddrm~IH~~~~~~~~~~~~~dyF~NYF~lGlDiLfd~~th~v~KiIL ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~iG~s~~~v~~~~G~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~g~v~~i~~ ", ) self.assertEqual(alignment.target.id, "U5LAW6_9BACI/1") self.assertEqual( alignment.target.seq[61:128], "FHIGQPVSEIYSSVFIDTNINFQYKGSSYRFELSEDDLNTRPLIKAGNIYAQLYIDRFTGELSSIRY", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF14504.5") self.assertEqual( alignment.target.annotations["hmm_description"], "; CAP_assoc_N ; CAP-associated N-terminal", ) self.assertEqual( alignment[0], "FHIGQPVSEIYSSVFIDTNINFQYKGSSYRFELSE-------------DDLNTRPLIKAGNIYAQLYIDRFTGELSSIRY", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ccCCCcHHHHHHhhCCCceEEEEEcCeEEEEEECcchhceeeeEEECCEEEEEEEeCCCCEEEEEEE ", ) self.assertEqual( str(alignment), """\ U5LAW6_9B 61 FHIGQPVSEIYSSVFIDTNINFQYKGSSYRFELSE-------------DDLNTRPLIKAG 0 ...|.......|........---------......-------------............ sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV---------FYKSEDKMKIHSPSPHKQVPSKCNDYFFNYF U5LAW6_9B 108 NIYAQLYIDRFTGELSSIRY 128 60 ........|..|........ 80 sp|Q9BSU1 289 TLGVDILFDANTHKVKKFVL 309 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 61, 81, 90, 96, 96, 128], [238, 258, 258, 264, 277, 309]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['F', 'H', 'I', 'G', 'Q', 'P', 'V', 'S', 'E', 'I', 'Y', 'S', 'S', 'V', 'F', 'I', 'D', 'T', 'N', 'I', 'N', 'F', 'Q', 'Y', 'K', 'G', 'S', 'S', 'Y', 'R', 'F', 'E', 'L', 'S', 'E', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'D', 'D', 'L', 'N', 'T', 'R', 'P', 'L', 'I', 'K', 'A', 'G', 'N', 'I', 'Y', 'A', 'Q', 'L', 'Y', 'I', 'D', 'R', 'F', 'T', 'G', 'E', 'L', 'S', 'S', 'I', 'R', 'Y'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'F', 'Y', 'K', 'S', 'E', 'D', 'K', 'M', 'K', 'I', 'H', 'S', 'P', 'S', 'P', 'H', 'K', 'Q', 'V', 'P', 'S', 'K', 'C', 'N', 'D', 'Y', 'F', 'F', 'N', 'Y', 'F', 'T', 'L', 'G', 'V', 'D', 'I', 'L', 'F', 'D', 'A', 'N', 'T', 'H', 'K', 'V', 'K', 'K', 'F', 'V', 'L']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 36.58) self.assertAlmostEqual(alignment.annotations["E-value"], 21) self.assertAlmostEqual(alignment.annotations["Score"], 24.91) self.assertAlmostEqual(alignment.annotations["Identities"], 23) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.342) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 4.700) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEEECCEEecCCCCCCcHhHHHhhcCCCCC ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[87:117], "KLKYCGVHFNSQAIAPTIEQIDQSFGATHP") self.assertEqual(alignment[1], "KLKYCGVHFNSQAIAPTIEQIDQSFGATHP") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~L~Y~g~~~~~~~~~pT~~~I~~~FGPTyP ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~F~~~g~~L~DP~P~~spe~V~~~ya~~yP ", ) self.assertEqual(alignment.target.id, "H8H183_DEIGI/2") self.assertEqual(alignment.target.seq[4:34], "VFKFDGKVLDDPNPKSTPEQVKTFYAPTYP") self.assertEqual(alignment.target.annotations["hmm_name"], "PF14454.5") self.assertEqual( alignment.target.annotations["hmm_description"], "; Prok_Ub ; Prokaryotic Ubiquitin", ) self.assertEqual(alignment[0], "VFKFDGKVLDDPNPKSTPEQVKTFYAPTYP") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " EEEECCEEccCCCCCCCHHHHHHHHHhhCH ", ) self.assertEqual( str(alignment), """\ H8H183_DE 4 VFKFDGKVLDDPNPKSTPEQVKTFYAPTYP 34 0 ..|..|..........|.||.......|.| 30 sp|Q9BSU1 87 KLKYCGVHFNSQAIAPTIEQIDQSFGATHP 117 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 4, 34], [ 87, 117]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['V', 'F', 'K', 'F', 'D', 'G', 'K', 'V', 'L', 'D', 'D', 'P', 'N', 'P', 'K', 'S', 'T', 'P', 'E', 'Q', 'V', 'K', 'T', 'F', 'Y', 'A', 'P', 'T', 'Y', 'P'], ['K', 'L', 'K', 'Y', 'C', 'G', 'V', 'H', 'F', 'N', 'S', 'Q', 'A', 'I', 'A', 'P', 'T', 'I', 'E', 'Q', 'I', 'D', 'Q', 'S', 'F', 'G', 'A', 'T', 'H', 'P']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 35.95) self.assertAlmostEqual(alignment.annotations["E-value"], 1.3e02) self.assertAlmostEqual(alignment.annotations["Score"], 23.17) self.assertAlmostEqual(alignment.annotations["Identities"], 12) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.155) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " ccccCCCCceEEcCCcHHHHHHHHHHccCccccEEEEECCCCCcCCCeEEEecCCCeEEEeccccCceeEEEEecCCCCEEEECCEEecCCCCCCcHhHHHhhcCCCCCCCccCccceEEeeeCeEEEEeeCcccCCCCccCCCcccccccCCCCCCCeEEEEEEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[8:174], "ERSLGNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKRMYIY", ) self.assertEqual( alignment[1], "ERSLGNEQWEFTLGMP-LAQAVAILQKHCRIIKNVQVLYSEQSPLSHD-------LILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFR-G----LSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKRMYIY", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " g~~LG~~~~~f~LG~sL~~vi~~Lr~~~~~~~~Vel~Ys~~~Pl~~dIvi~L~~~GirL~Fd~~~QrL~lIEV~d~s~v~L~Y~g~~~~~~~~~pT~~~I~~~FGPTyPG~yd~~~~~Y~LsYpGisF~Fpi~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~m~If ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " G~~~~~~~~ig~s~~~eV~~~~G~P~~~~~~~~~~g~y~~y~~~~~~fg~~~~~~i~~ir~~~~~l~~lt~~~ikk~LG~P~~~~~~~g~~~~~Y~~g~~y~L~f~~~~~~~~~~~~~v~hi~l~", ) self.assertEqual(alignment.target.id, "R4K5N0_CLOPA/8") self.assertEqual( alignment.target.seq[10:135], "GKVFNSDFPAKDTNIDSVESKWGKADNSEWVASAKGLYSTYSKHNIVFGSNKGGQIFEVRSLDKQLGNIYLSMVKDKLGTPQHDVKVNGEEIIGYKMGNDFKILFVFPEPTNQHANPIMSHYSVL", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF14172.5") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF4309 ; Domain of unknown function (DUF4309)", ) self.assertEqual( alignment[0], "GKVFNS---DFPAKDTNIDSVESKW----------------GKADNSEWVASAKGLYSTYSKHNIVFGSNKGGQ---IFEVRSL------------DKQLGNIYLSMVKDKLGT--PQHDVKVNGEEIIGYKMGNDFKILFVFPEPTNQ------------------HANPIMSHYSVL", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCCCCCCCCCCCCcHHHHHHHhCCCCceehhhhcCCeeEEEeCCeEEEEECCCCcEEEEEEeCccccccCHHHHHHhhCCCceEEEECCEEEEEEEcCCCEEEEEEeCCCCCCCCCCceeEEEeC", ) self.assertEqual( str(alignment), """\ R4K5N0_CL 10 GKVFNS---DFPAKDTNIDSVESKW----------------GKADNSEWVASAKGLYSTY 0 ......---.|.....-........----------------.......-------|.... sp|Q9BSU1 8 ERSLGNEQWEFTLGMP-LAQAVAILQKHCRIIKNVQVLYSEQSPLSHD-------LILNL R4K5N0_CL 51 SKHNIVFGSNKGGQ---IFEVRSL------------DKQLGNIYLSMVKDKLGT--PQHD 60 ....|........|---..||..|------------..|.............|.--|... sp|Q9BSU1 60 TQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIAPTIEQIDQSFGATHPGVY R4K5N0_CL 94 VKVNGEEIIGYKMGNDFKILFVFPEPTNQ------------------HANPIMSHYSVL 120 ............-|----..|.|......------------------............ sp|Q9BSU1 120 NSAEQLFHLNFR-G----LSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKRMYIY R4K5N0_CL 135 179 sp|Q9BSU1 174 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 10, 16, 16, 23, 24, 32, 32, 39, 46, 65, 65, 72, 72, 90, 90, 106, 107, 108, 112, 123, 123, 135], [ 8, 14, 17, 24, 24, 32, 48, 55, 55, 74, 77, 84, 96, 114, 116, 132, 132, 133, 133, 144, 162, 174]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'K', 'V', 'F', 'N', 'S', '-', '-', '-', 'D', 'F', 'P', 'A', 'K', 'D', 'T', 'N', 'I', 'D', 'S', 'V', 'E', 'S', 'K', 'W', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'K', 'A', 'D', 'N', 'S', 'E', 'W', 'V', 'A', 'S', 'A', 'K', 'G', 'L', 'Y', 'S', 'T', 'Y', 'S', 'K', 'H', 'N', 'I', 'V', 'F', 'G', 'S', 'N', 'K', 'G', 'G', 'Q', '-', '-', '-', 'I', 'F', 'E', 'V', 'R', 'S', 'L', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'D', 'K', 'Q', 'L', 'G', 'N', 'I', 'Y', 'L', 'S', 'M', 'V', 'K', 'D', 'K', 'L', 'G', 'T', '-', '-', 'P', 'Q', 'H', 'D', 'V', 'K', 'V', 'N', 'G', 'E', 'E', 'I', 'I', 'G', 'Y', 'K', 'M', 'G', 'N', 'D', 'F', 'K', 'I', 'L', 'F', 'V', 'F', 'P', 'E', 'P', 'T', 'N', 'Q', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'H', 'A', 'N', 'P', 'I', 'M', 'S', 'H', 'Y', 'S', 'V', 'L'], ['E', 'R', 'S', 'L', 'G', 'N', 'E', 'Q', 'W', 'E', 'F', 'T', 'L', 'G', 'M', 'P', '-', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', '-', '-', '-', '-', '-', '-', '-', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'C', 'D', 'L', 'T', 'K', 'V', 'K', 'L', 'K', 'Y', 'C', 'G', 'V', 'H', 'F', 'N', 'S', 'Q', 'A', 'I', 'A', 'P', 'T', 'I', 'E', 'Q', 'I', 'D', 'Q', 'S', 'F', 'G', 'A', 'T', 'H', 'P', 'G', 'V', 'Y', 'N', 'S', 'A', 'E', 'Q', 'L', 'F', 'H', 'L', 'N', 'F', 'R', '-', 'G', '-', '-', '-', '-', 'L', 'S', 'F', 'S', 'F', 'Q', 'L', 'D', 'S', 'W', 'T', 'E', 'A', 'P', 'K', 'Y', 'E', 'P', 'N', 'F', 'A', 'H', 'G', 'L', 'A', 'S', 'L', 'Q', 'I', 'P', 'H', 'G', 'A', 'T', 'V', 'K', 'R', 'M', 'Y', 'I', 'Y']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 33.21) self.assertAlmostEqual(alignment.annotations["E-value"], 69) self.assertAlmostEqual(alignment.annotations["Score"], 26.69) self.assertAlmostEqual(alignment.annotations["Identities"], 17) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.109) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 5.600) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CCCCceEEcCCcHHHHHHHHHHccCccccEEEEECCCCCcCCCeEEEecCCCeEEEecccc ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[12:73], "GNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFN", ) self.assertEqual( alignment[1], "GNEQWEFTLGMPLAQAVAILQKHCRIIK--NVQVLYSE-----QSPLSHDLILNLTQDGIKLMFDAFN", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " G~~~~~f~LG~sL~~vi~~Lr~~~~~~~~Vel~Ys~~~Pl~~dIvi~L~~~GirL~Fd~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " GwEHiE~Vvp~~~~~~~~~~~~~~~~~~~~~i~~k~s~pk~~~erl~NPtva~~~~~~~iKfHp~s ", ) self.assertEqual(alignment.target.id, "Q7N560_PHOLL/9") self.assertEqual( alignment.target.seq[101:167], "GWEHVELVLPVAPEILSTAAKALLPQPLPAGFSVKESQPKGEQERLPNPTLAITDGEITVKFHPFT", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF06185.11") self.assertEqual( alignment.target.annotations["hmm_description"], "; YecM ; YecM protein" ) self.assertEqual( alignment[0], "GWEHVELVLPVAPEILSTAAKALLPQPLPAGFSVKESQPKGEQERLPNPTLAITD--GEITVKFHPFT", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CeeEEEEEecCChHHHHHHHHHHCCCCCCCCcEEEEecCCCcccCCCCceEEEEcCCEEEEEccCC ", ) self.assertEqual( str(alignment), """\ Q7N560_PH 101 GWEHVELVLPVAPEILSTAAKALLPQPLPAGFSVKESQPKGEQERLPNPTLAITD--GEI 0 |.|..|..|...................--...|..|.-----.......|....--..| sp|Q9BSU1 12 GNEQWEFTLGMPLAQAVAILQKHCRIIK--NVQVLYSE-----QSPLSHDLILNLTQDGI Q7N560_PH 159 TVKFHPFT 167 60 ...|..|. 68 sp|Q9BSU1 65 KLMFDAFN 73 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[101, 129, 131, 139, 144, 156, 156, 167], [ 12, 40, 40, 48, 48, 60, 62, 73]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'W', 'E', 'H', 'V', 'E', 'L', 'V', 'L', 'P', 'V', 'A', 'P', 'E', 'I', 'L', 'S', 'T', 'A', 'A', 'K', 'A', 'L', 'L', 'P', 'Q', 'P', 'L', 'P', 'A', 'G', 'F', 'S', 'V', 'K', 'E', 'S', 'Q', 'P', 'K', 'G', 'E', 'Q', 'E', 'R', 'L', 'P', 'N', 'P', 'T', 'L', 'A', 'I', 'T', 'D', '-', '-', 'G', 'E', 'I', 'T', 'V', 'K', 'F', 'H', 'P', 'F', 'T'], ['G', 'N', 'E', 'Q', 'W', 'E', 'F', 'T', 'L', 'G', 'M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', 'K', '-', '-', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', '-', '-', '-', '-', '-', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 30.70) self.assertAlmostEqual(alignment.annotations["E-value"], 18) self.assertAlmostEqual(alignment.annotations["Score"], 28.76) self.assertAlmostEqual(alignment.annotations["Identities"], 30) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.610) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.300) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEeCCchHHHHHhhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~fG~T~QDVl~~LG~P~~v ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~~Gmt~~eV~~~lG~P~~~ ", ) self.assertEqual(alignment.target.id, "Q8DTX1_STRMU/4") self.assertEqual(alignment.target.seq[94:114], "LKIGESYKKVVEKLGEPDVL") self.assertEqual(alignment.target.annotations["hmm_name"], "PF12978.6") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF3862 ; Domain of Unknown Function with PDB structure (DUF3862)", ) self.assertEqual(alignment[0], "LKIGESYKKVVEKLGEPDVL") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCCCCCHHHHHHHHCCCCee ", ) self.assertEqual( str(alignment), """\ Q8DTX1_ST 94 LKIGESYKKVVEKLGEPDVL 114 0 ...|.|...|...||.|... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 94, 114], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'K', 'I', 'G', 'E', 'S', 'Y', 'K', 'K', 'V', 'V', 'E', 'K', 'L', 'G', 'E', 'P', 'D', 'V', 'L'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 29.70) self.assertAlmostEqual(alignment.annotations["E-value"], 83) self.assertAlmostEqual(alignment.annotations["Score"], 23.66) self.assertAlmostEqual(alignment.annotations["Identities"], 22) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.238) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.700) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CCCCceEEcCCcHHHHHHHHHHccCccccEEEEECCCCCcCCCeEEEecCCCeEEEeccccCceeEEEEec ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[12:83], "GNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCD", ) self.assertEqual( alignment[1], "GNEQWEFTLGMPLAQAVAILQKHCRI-----IKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCD", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " G~~~~~f~LG~sL~~vi~~Lr~~~~~~~~Vel~Ys~~~Pl~~dIvi~L~~~GirL~Fd~~~QrL~lIEV~d ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " gi~iG~s~~~v~~~~G~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~g~v~~i~~~~ ", ) self.assertEqual(alignment.target.id, "U5LAW6_9BACI/1") self.assertEqual( alignment.target.seq[60:130], "PFHIGQPVSEIYSSVFIDTNINFQYKGSSYRFELSEDDLNTRPLIKAGNIYAQLYIDRFTGELSSIRYMD", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF14504.5") self.assertEqual( alignment.target.annotations["hmm_description"], "; CAP_assoc_N ; CAP-associated N-terminal", ) self.assertEqual( alignment[0], "P-----FHIGQPVSEIYSSVFIDTNINFQYKGSSYRFELSEDDLNTRPLIKA-GNIYAQLYIDRFTGELSSIRYMD", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CccCCCcHHHHHHhhCCCceEEEEEcCeEEEEEECcchhceeeeEEECCEEEEEEEeCCCCEEEEEEEec ", ) self.assertEqual( str(alignment), """\ U5LAW6_9B 60 P-----FHIGQPVSEIYSSVFIDTNINFQYKGSSYRFELSEDDLNTRPLIKA-GNIYAQL 0 .-----|..|.|.............|-----........||.......||..-......| sp|Q9BSU1 12 GNEQWEFTLGMPLAQAVAILQKHCRI-----IKNVQVLYSEQSPLSHDLILNLTQDGIKL U5LAW6_9B 114 YIDRFTGELSSIRYMD 130 60 ..|.|...|..|...| 76 sp|Q9BSU1 67 MFDAFNQRLKVIEVCD 83 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 60, 61, 61, 81, 86, 107, 107, 130], [ 12, 13, 18, 38, 38, 59, 60, 83]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['P', '-', '-', '-', '-', '-', 'F', 'H', 'I', 'G', 'Q', 'P', 'V', 'S', 'E', 'I', 'Y', 'S', 'S', 'V', 'F', 'I', 'D', 'T', 'N', 'I', 'N', 'F', 'Q', 'Y', 'K', 'G', 'S', 'S', 'Y', 'R', 'F', 'E', 'L', 'S', 'E', 'D', 'D', 'L', 'N', 'T', 'R', 'P', 'L', 'I', 'K', 'A', '-', 'G', 'N', 'I', 'Y', 'A', 'Q', 'L', 'Y', 'I', 'D', 'R', 'F', 'T', 'G', 'E', 'L', 'S', 'S', 'I', 'R', 'Y', 'M', 'D'], ['G', 'N', 'E', 'Q', 'W', 'E', 'F', 'T', 'L', 'G', 'M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', '-', '-', '-', '-', '-', 'I', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'C', 'D']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 28.54) self.assertAlmostEqual(alignment.annotations["E-value"], 1.2e02) self.assertAlmostEqual(alignment.annotations["Score"], 22.65) self.assertAlmostEqual(alignment.annotations["Identities"], 18) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.331) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 4.100) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CcHHHHHHHHHHccCccccEEEEECCCCCcCCCeEEEecCCCeEEEeccccCceeEEEEe ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual( alignment.query.seq[22:82], "MPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVC", ) self.assertEqual( alignment[1], "MPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNL----TQDGIKLMFDAFNQRLK-VIEVC", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~sL~~vi~~Lr~~~~~~~~Vel~Ys~~~Pl~~dIvi~L~~~GirL~Fd~~~QrL~lIEV~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " m~~eE~ieYi~~nV~~gD~lEisy~Rv~vpGeVi~i~~~~~~~~~~~~~~l~l~ge~~~~~vevD ", ) self.assertEqual(alignment.target.id, "A5UN43_METS3/2") self.assertEqual( alignment.target.seq[4:69], "LTPDKAVEYLKDNVKIHDNLEISYNRIFGSGEVLNMDFSEYFGKPGFKMLLSLDGDSINPTIEID", ) self.assertEqual(alignment.target.annotations["hmm_name"], "PF09870.8") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF2097 ; Uncharacterized protein conserved in archaea (DUF2097)", ) self.assertEqual( alignment[0], "LTPDKAVEYLKDNVKIHDNLEISYNRIFGSGEVLNMDFSEYFGKPGFKMLLSLDGDSINPTIEID", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " CCHHHHHHHHHHhCCcCCeEEEEeceeeeeeeEEEEecccccCCCcEEEEEEECCCcccceEEEe ", ) self.assertEqual( str(alignment), """\ A5UN43_ME 4 LTPDKAVEYLKDNVKIHDNLEISYNRIFGSGEVLNMDFSEYFGKPGFKMLLSLDGDSINP 0 .....||..|.....|..|....|.........|....----...|.|...........- sp|Q9BSU1 22 MPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNL----TQDGIKLMFDAFNQRLK- A5UN43_ME 64 TIEID 69 60 .||.. 65 sp|Q9BSU1 77 VIEVC 82 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 4, 42, 46, 63, 64, 69], [22, 60, 60, 77, 77, 82]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'T', 'P', 'D', 'K', 'A', 'V', 'E', 'Y', 'L', 'K', 'D', 'N', 'V', 'K', 'I', 'H', 'D', 'N', 'L', 'E', 'I', 'S', 'Y', 'N', 'R', 'I', 'F', 'G', 'S', 'G', 'E', 'V', 'L', 'N', 'M', 'D', 'F', 'S', 'E', 'Y', 'F', 'G', 'K', 'P', 'G', 'F', 'K', 'M', 'L', 'L', 'S', 'L', 'D', 'G', 'D', 'S', 'I', 'N', 'P', 'T', 'I', 'E', 'I', 'D'], ['M', 'P', 'L', 'A', 'Q', 'A', 'V', 'A', 'I', 'L', 'Q', 'K', 'H', 'C', 'R', 'I', 'I', 'K', 'N', 'V', 'Q', 'V', 'L', 'Y', 'S', 'E', 'Q', 'S', 'P', 'L', 'S', 'H', 'D', 'L', 'I', 'L', 'N', 'L', '-', '-', '-', '-', 'T', 'Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', '-', 'V', 'I', 'E', 'V', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 26.31) self.assertAlmostEqual(alignment.annotations["E-value"], 22) self.assertAlmostEqual(alignment.annotations["Score"], 28.97) self.assertAlmostEqual(alignment.annotations["Identities"], 20) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.378) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.400) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEeCCchHHHHHhhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~fG~T~QDVl~~LG~P~~v ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~~G~t~~eV~~~lG~p~~~ ", ) self.assertEqual(alignment.target.id, "Q9KJ90_STREX/2") self.assertEqual(alignment.target.seq[39:59], "IQFGMTFDEVWEIGGGEAAC") self.assertEqual(alignment.target.annotations["hmm_name"], "PF07467.10") self.assertEqual( alignment.target.annotations["hmm_description"], "; BLIP ; Beta-lactamase inhibitor (BLIP)", ) self.assertEqual(alignment[0], "IQFGMTFDEVWEIGGGEAAC") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCCCCCHHHHHHHhCCCCee ", ) self.assertEqual( str(alignment), """\ Q9KJ90_ST 39 IQFGMTFDEVWEIGGGEAAC 59 0 ..||.....|....|..... 20 sp|Q9BSU1 238 VYFGDSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 39, 59], [238, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'Q', 'F', 'G', 'M', 'T', 'F', 'D', 'E', 'V', 'W', 'E', 'I', 'G', 'G', 'G', 'E', 'A', 'A', 'C'], ['V', 'Y', 'F', 'G', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 25.89) self.assertAlmostEqual(alignment.annotations["E-value"], 32) self.assertAlmostEqual(alignment.annotations["Score"], 27.15) self.assertAlmostEqual(alignment.annotations["Identities"], 20) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.380) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 9.300) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " EEeCCchHHHHHhhcCCcEE ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[238:258], "VYFGDSCQDVLSMLGSPHKV") self.assertEqual(alignment[1], "VYFG---------DSCQDVLSMLGSPHKV") self.assertEqual( alignment.query.letter_annotations["Consensus"], " I~fG~T~QDVl~~LG~P~~v ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " i~~g~~~~~~~~g~t~~~V~~~~G~p~~~ ", ) self.assertEqual(alignment.target.id, "Q8DTX1_STRMU/4") self.assertEqual(alignment.target.seq[11:40], "IKVTTDQNHFSGGTSIEQLKQWFGDPNKS") self.assertEqual(alignment.target.annotations["hmm_name"], "PF12978.6") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF3862 ; Domain of Unknown Function with PDB structure (DUF3862)", ) self.assertEqual(alignment[0], "IKVTTDQNHFSGGTSIEQLKQWFGDPNKS") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " eeecCcccCCCCCCCHHHHHHHHCCCceE ", ) self.assertEqual( str(alignment), """\ Q8DTX1_ST 11 IKVTTDQNHFSGGTSIEQLKQWFGDPNKS 40 0 ....---------.|........|.|.|. 29 sp|Q9BSU1 238 VYFG---------DSCQDVLSMLGSPHKV 258 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 11, 15, 24, 40], [238, 242, 242, 258]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'K', 'V', 'T', 'T', 'D', 'Q', 'N', 'H', 'F', 'S', 'G', 'G', 'T', 'S', 'I', 'E', 'Q', 'L', 'K', 'Q', 'W', 'F', 'G', 'D', 'P', 'N', 'K', 'S'], ['V', 'Y', 'F', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'D', 'S', 'C', 'Q', 'D', 'V', 'L', 'S', 'M', 'L', 'G', 'S', 'P', 'H', 'K', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 20.88) self.assertAlmostEqual(alignment.annotations["E-value"], 78) self.assertAlmostEqual(alignment.annotations["Score"], 19.81) self.assertAlmostEqual(alignment.annotations["Identities"], 26) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.368) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 0.0) self.assertAlmostEqual(alignment.annotations["Template_Neff"], 7.400) self.assertEqual( alignment.query.letter_annotations["ss_pred"], " CCCeEEEeccccCceeEEEEecCC ", ) self.assertEqual( alignment.query.id, "sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70 PE=1 SV=1", ) self.assertEqual(alignment.query.seq[61:85], "QDGIKLMFDAFNQRLKVIEVCDLT") self.assertEqual(alignment[1], "QDGIKLMFDAFNQRLKVIEVCDLT") self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~GirL~Fd~~~QrL~lIEV~d~s ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~i~ld~d~~g~ivgiEil~~s", ) self.assertEqual(alignment.target.id, "Q21BS2_RHOPB/5") self.assertEqual(alignment.target.seq[25:48], "APNVIFDYDAEGRIVGIELLDAR") self.assertEqual(alignment.target.annotations["hmm_name"], "PF10049.8") self.assertEqual( alignment.target.annotations["hmm_description"], "; DUF2283 ; Protein of unknown function (DUF2283)", ) self.assertEqual(alignment[0], "APNVIFDYDA-EGRIVGIELLDAR") self.assertEqual( alignment.target.letter_annotations["ss_pred"], " cCCEEEEECCCCCEEEEEEEecC", ) self.assertEqual( str(alignment), """\ Q21BS2_RH 25 APNVIFDYDA-EGRIVGIELLDAR 48 0 ........||-..|...||..|.. 24 sp|Q9BSU1 61 QDGIKLMFDAFNQRLKVIEVCDLT 85 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[25, 35, 35, 48], [61, 71, 72, 85]]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'P', 'N', 'V', 'I', 'F', 'D', 'Y', 'D', 'A', '-', 'E', 'G', 'R', 'I', 'V', 'G', 'I', 'E', 'L', 'L', 'D', 'A', 'R'], ['Q', 'D', 'G', 'I', 'K', 'L', 'M', 'F', 'D', 'A', 'F', 'N', 'Q', 'R', 'L', 'K', 'V', 'I', 'E', 'V', 'C', 'D', 'L', 'T']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_length(self): """Test getting the number of alignments without parsing the file.""" stream = open(self.path) alignments = Align.parse(stream, "hhr") stream.close() self.assertEqual(len(alignments), 16) class Align_hhr_2uvo_hhblits_emptytable(unittest.TestCase): path = os.path.join("HHsuite", "2uvo_hhblits_emptytable.hhr") def test_reading(self): alignments = Align.parse(self.path, "hhr") self.assertEqual(alignments.metadata["Match_columns"], 171) self.assertEqual(alignments.metadata["No_of_seqs"], (1560, 4005)) self.assertAlmostEqual(alignments.metadata["Neff"], 8.3) self.assertEqual(alignments.metadata["Searched_HMMs"], 34) self.assertEqual(alignments.metadata["Rundate"], "Fri Feb 15 16:34:13 2019") with self.assertRaises(StopIteration): next(alignments) def test_length(self): """Test getting the number of alignments without parsing the file.""" stream = open(self.path) alignments = Align.parse(stream, "hhr") stream.close() self.assertEqual(len(alignments), 0) class Align_hhr_2uvo_hhblits_onlyheader(unittest.TestCase): path = os.path.join("HHsuite", "2uvo_hhblits_onlyheader.hhr") def test_reading(self): with self.assertRaises(ValueError) as cm: alignments = Align.parse(self.path, "hhr") self.assertEqual(str(cm.exception), "Truncated file.") class Align_hhr_7rbx_A_hhsearch_trunc(unittest.TestCase): path = os.path.join("HHsuite", "7rbx_A_hhsearch_trunc.hhr") def test_reading(self): alignments = Align.parse(self.path, "hhr") self.assertEqual(alignments.metadata["No_of_seqs"], (336, 10000)) self.assertAlmostEqual(alignments.metadata["Neff"], 5.31565) self.assertEqual(alignments.metadata["Searched_HMMs"], 90139) self.assertEqual(alignments.metadata["Rundate"], "Fri Dec 24 23:14:30 2021") self.assertEqual( alignments.metadata["Command line"], "/mnt/home/dberenberg/gustaf_stuff/hh-suite/build/bin/hhsearch -i /tmp/tmprgvo26zr/query.a3m -o /tmp/tmprgvo26zr/output.hhr -maxseq 1000000 -cpu 2 -d /mnt/home/dberenberg/gustaf_stuff/OpenFold/pdb70/pdb70", ) alignment = next(alignments) self.assertAlmostEqual(alignment.annotations["Probab"], 100.00) self.assertAlmostEqual(alignment.annotations["E-value"], 1.8e-115, places=116) self.assertAlmostEqual(alignment.annotations["Score"], 931.2) self.assertAlmostEqual(alignment.annotations["Identities"], 36.0) self.assertAlmostEqual(alignment.annotations["Similarity"], 0.615) self.assertAlmostEqual(alignment.annotations["Sum_probs"], 412.8) self.assertEqual(alignment.query.id, "query") self.assertEqual( alignment.query.seq[12:-1], "EAQTQGPGSMTDFYSLIPSAPKGRFDGIERAHTAEDVKRLRGSVEIKYSLAEMGANRLWKLIHEEDFVNALGALSGNQAMQMVRAGLKAIYLSGWQVAADANTASAMYPDQSLYPANAGPELAKRINRTLQRADQIETAEGKGLSVDTWFAPIVADAEAGFGGPLDAFEIMKAYIEAGAAGVHFEDQLASEKKCGHLGGKVLIPTAAHIRNLNAARLAADVMGTPTLIVARTDAEAAKLLTSDIDERDQPFVDYEAGRTAEGFYQVKNGIEPCIARAIAYAPYCDLIWMETSKPDLAQARRFAEAVHKAHPGKLLAYNCSPSFNWKKNLDDATIAKFQRELGAMGYKFQFITLAGFHQLNYGMFELARGYKDRQMAAYSELQQAEFAAEADGYTATKHQREVGTGYFDAVSLAITGGQSSTTAMKESTETAQFKPAA", ) self.assertEqual( alignment[1], "EAQTQGPGSMTDFYSLIPSAPKGRFDGIERAHTAEDVKRLRGSVEIKYSLAEMGANRLWKLIHE----EDFVNALGALSGNQAMQMVRAGLKAIYLSGWQVAADANTASAMYPDQSLYPANAGPELAKRINRTLQRADQIETAEGKG--------LSVDTWFAPIVADAEAGFGGPLDAFEIMKAYIEAGAAGVHFEDQLASEKKCGHLGGKVLIPTAAHIRNLNAARLAADVMGTPTLIVARTDAEAAKLLTSDIDERDQPFV------------------------------------------------------------------------------------------------DYEAGRTAEGFYQVKNGIEPCIARAIAYAPYCDLIWMETSKPDLAQARRFAEAVHKAHPGKLLAYNCSPSFNWKKNLDDATIAKFQRELGAMGYKFQFITLAGFHQLNYGMFELARGYKDRQMAAYSELQQAEFAAEADGYTATKHQREVGTGYFDAVSLAITGGQSSTTAMKESTETAQFKPAA", ) self.assertEqual( alignment.query.letter_annotations["Consensus"], " ~~~~~~~~~~~~~~~~~~~~~~~R~~~i~R~ysa~~V~~lrgs~~~~~~~a~~~a~kL~~ll~~~~~~~~~Ga~~~~~a~~~~~ag~~aiYvSG~~~a~~a~~~~~~~PD~~~yp~~tvp~~v~~i~~~~~~~~~~~~~e~~~~~~~~~~~PiiaDaDtG~Gg~~~~~~~~k~~ieaGaAgih~EDQ~~~~KrCGh~~gK~lvp~~e~i~~l~Aa~~a~d~~~~~~~iiARTDA~aa~ll~s~id~rd~~Fid~ea~RT~EGfy~~k~gle~AIaRalA~Ap~aDliW~Et~kPdl~~A~~FAe~V~~~~P~k~LaYN~SpSFnw~~~~~d~~i~~f~~eLa~lGy~~QfitLAGfh~~~~~~~~lA~~~~~~gm~aYvelqq~e~~~~~~g~~~~~HQ~~~G~~y~D~~~~~i~gg~~st~a~~~ste~~qf~~~~ ", ) self.assertEqual( alignment.target.letter_annotations["Consensus"], " ~~~~~~~~~~~~v~~i~~~~~~~R~~~i~R~Yta~~V~~lRgs~~~~~~~~~~a~kL~~lL~~~~~~~~~~~~~Ga~D~~sA~~~a~Gf~aiyvSG~~vSa~~g~~~~~~PD~~~~p~~ev~~~v~rI~~a~~~~Dr~q~~~~~~~~~~~r~~~~~~d~~~PIIAD~DtGfGg~~~v~~lvk~~~eAGaAGIhIEDq~~g~Kkcgh~~gk~Lvp~~e~~~RL~AAr~a~d~~g~d~vIiARTDA~~a~li~s~~D~rDh~~I~G~~~~~~~~l~~al~ra~~~g~~~~ei~~~~~~w~~~~~Ltty~e~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~r~~a~~~~~~~~~~dwd~~Rt~eG~Y~~~~g~~~aI~Ra~a~apyaDllW~Et~~P~~~~a~~Fa~~i~~~~P~~~laYN~SpSFnW~~~~~~~~~~~f~~~L~klG~~~qfitlag~h~~~~~~~~~a~~~~~~gm~aYv~~vQr~e~~~g~~~~~HQ~wsGa~~~D~~~~~v~~g~sst~a~g~~~te~qf~~~~ ", ) self.assertEqual(alignment.target.id, "7EBE_A") self.assertEqual( alignment.target.seq[12:-3], "DIQKEEADFQKEVAEIKKWWSEPRWRKTKRIYSAEDIAKKRGTLKINHPSSQQADKLFKLLEKHDADKTVSFTFGALDPIHVAQMAKYLDSIYVSGWQCSSTASTSNEPSPDLADYPMDTVPNKVEHLWFAQLFHDRKQREERLTLSKEERAKTPYIDFLRPIIADADTGHGGITAIIKLTKMFIERGAAGIHIEDQAPGTKKCGHMAGKVLVPVQEHINRLVAIRASADIFGSNLLAVARTDSEAATLITSTIDHRDHYFIIGATNPEAGDLAALMAEAESKGIYGNELAAIESEWTKKAGLKLFHEAVIDEIKNGNYSNKDALIKKFTDKVNPLSHTSHKEAKKLAKELTGKDIYFNWDVARAREGYYRYQGGTQCAVMRGRAFAPYADLIWMESALPDYAQAKEFADGVKAAVPDQWLAYNLSPSFNWNKAMPADEQETYIKRLGKLGYVWQFITLAGLHTTALAVDDFSNQYSQIGMKAYGQTVQQPEIEKGVEVVKHQKWSGATYIDGLLKMVSGGVTSTAAMGQGVTEDQFKESK", ) self.assertEqual(alignment.target.annotations["hmm_name"], "7EBE_A") self.assertEqual( alignment.target.annotations["hmm_description"], "Isocitrate lyase (E.C.4.1.3.1); Isocitrate lyase, glyoxylate cycle, ubiquitination; HET: FMT; 2.69A {Candida albicans}", ) self.assertEqual( alignment[0], "DIQKEEADFQKEVAEIKKWWSEPRWRKTKRIYSAEDIAKKRGTLKINH-PSSQQADKLFKLLEKHDADKTVSFTFGALDPIHVAQMAK-YLDSIYVSGWQCSSTASTSNEPSPDLADYPMDTVPNKVEHLWFAQLFHDRKQREERLTLSKEERAKTPYIDFLRPIIADADTGHGGITAIIKLTKMFIERGAAGIHIEDQAPGTKKCGHMAGKVLVPVQEHINRLVAIRASADIFGSNLLAVARTDSEAATLITSTIDHRDHYFIIGATNPEAGDLAALMAEAESKGIYGNELAAIESEWTKKAGLKLFHEAVIDEIKNGNYSNKDALIKKFTDKVNPLSHTSHKEAKKLAKELTGKDIYFNWDVARAREGYYRYQGGTQCAVMRGRAFAPYADLIWMESALPDYAQAKEFADGVKAAVPDQWLAYNLSPSFNWNKAMPADEQETYIKRLGKLGYVWQFITLAGLHTTALAVDDFSNQYSQIGMKAYGQTVQQPE--IEKGVEVVKHQKWSGATYIDGLLKMVSGGVTSTAAMGQGVTEDQFKESK", ) self.assertEqual( alignment.target.letter_annotations["ss_dssp"], " CHHHHHHHHHHHHHHHHHHHTSGGGTTCCCCSCHHHHHTTSCSSCCCCTHHHHHHHHHHHHHHHHHTTCCEEEEBCCSHHHHHHHTTTCSCEEECHHHHHHHCCTTSCCCSSSSCSCTTHHHHHHHHHHHHHHHHHHHHHHHHHTSCHHHHTTSCBCCCCCCEEEECTTCSSSHHHHHHHHHHHHHTTCSEEEEESBCTTSCCCTTSSCCEECCHHHHHHHHHHHHHHHHHHTCCCEEEEEECTTTCCEESCCCCGGGGGGBCEECCTTCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHTEECHHHHHHHHHHTSSCSSHHHHHHHHHHHSSTTSCCCHHHHHHHHHHHHSSCCCCBSSTTCCTTSCEEBCCCHHHHHHHHHHHGGGCSEEEECCSSCCHHHHHHHHHHHHTTCTTCEEEEECCTTSCHHHHSCHHHHHHHHHHHHHHTEEEEEETTHHHHHHHHHHHHHHHHHHHHTTHHHCCCCCHHHHHTTCGGGSHHHHHTHHHHHHHHHHHTTTCCTTCTTSTTCTTGGGC ", ) self.assertEqual( alignment.target.letter_annotations["ss_pred"], " ChhHHHHHHHHHHHHHHHHHhCcccccCCCCCCHHHHHHHhCCCCCCCcchHHHHHHHHHHHHcccCCCeEEEecCCCHHHHHHHHhcCCEEEEchhHHHHhccCCCCCCCCccCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHccCCCCCCCCcEEEeCCCCCCcHHHHHHHHHHHHHcCCCEEEeCCCCCCCCCCccCCCCeecCHHHHHHHHHHHHHHHHHhCCCEEEEEEecchhhhhhhccCCCCCcceeecCCCcccCcHHHHHHHHHHCCCCHHHHHHHHHHHhhhcCCccHhHHHHHHHHhCCCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHhCCCCcCCCCCCCcccccEEecccHHHHHHHHHHhccccCEEEEeCCCCCHHHHHHHHHHHHHHCCCCEEEEEeCCCCCcccCCCHHHHHHHHHHHHHcCCeEEEEechHHHHHHHHHHHHHHHHHHcCHHHHHHHcHHHHHHcCCcccccCccccchHHHHHHHHHhCCcchhhhccCCCchhhccchh ", ) self.assertEqual( alignment.column_annotations["Confidence"], " 334556778999999999999999999999999999999999999988888999999999985 689999999999999999979999999999999999877999999999999999999999999999999999987754 3456678999999999999999999999999999999999999998899999999999999999999999999999989999999Confidence 999999999999999999999876 78899999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999998 78899999999999999999999999999999999999999999876 ", ) self.assertEqual( str(alignment), """\ 7EBE_A 12 DIQKEEADFQKEVAEIKKWWSEPRWRKTKRIYSAEDIAKKRGTLKINH-PSSQQADKLFK 0 ..|....................|.....|...|||....||...|..-.....|..|.| query 12 EAQTQGPGSMTDFYSLIPSAPKGRFDGIERAHTAEDVKRLRGSVEIKYSLAEMGANRLWK 7EBE_A 71 LLEKHDADKTVSFTFGALDPIHVAQMAK-YLDSIYVSGWQCSSTASTSNEPSPDLADYPM 60 |...----.......|||......||..-.|..||.||||....|.|.....||...||. query 72 LIHE----EDFVNALGALSGNQAMQMVRAGLKAIYLSGWQVAADANTASAMYPDQSLYPA 7EBE_A 130 DTVPNKVEHLWFAQLFHDRKQREERLTLSKEERAKTPYIDFLRPIIADADTGHGGITAII 120 ...|.............|.....|...--------........||.|||..|.||..... query 128 NAGPELAKRINRTLQRADQIETAEGKG--------LSVDTWFAPIVADAEAGFGGPLDAF 7EBE_A 190 KLTKMFIERGAAGIHIEDQAPGTKKCGHMAGKVLVPVQEHINRLVAIRASADIFGSNLLA 180 ...|..||.||||.|.|||....|||||..||||.|...||..|.|.|..||..|...|. query 180 EIMKAYIEAGAAGVHFEDQLASEKKCGHLGGKVLIPTAAHIRNLNAARLAADVMGTPTLI 7EBE_A 250 VARTDSEAATLITSTIDHRDHYFIIGATNPEAGDLAALMAEAESKGIYGNELAAIESEWT 240 |||||.|||.|.||.||.||..|.------------------------------------ query 240 VARTDAEAAKLLTSDIDERDQPFV------------------------------------ 7EBE_A 310 KKAGLKLFHEAVIDEIKNGNYSNKDALIKKFTDKVNPLSHTSHKEAKKLAKELTGKDIYF 300 ------------------------------------------------------------ query 264 ------------------------------------------------------------ 7EBE_A 370 NWDVARAREGYYRYQGGTQCAVMRGRAFAPYADLIWMESALPDYAQAKEFADGVKAAVPD 360 .....|..||.|....|......|..|.|||.||||||...||.|||..||..|..|.|. query 264 DYEAGRTAEGFYQVKNGIEPCIARAIAYAPYCDLIWMETSKPDLAQARRFAEAVHKAHPG 7EBE_A 430 QWLAYNLSPSFNWNKAMPADEQETYIKRLGKLGYVWQFITLAGLHTTALAVDDFSNQYSQ 420 ..||||.||||||.|.............||..||..|||||||.|............|.. query 324 KLLAYNCSPSFNWKKNLDDATIAKFQRELGAMGYKFQFITLAGFHQLNYGMFELARGYKD 7EBE_A 490 IGMKAYGQTVQQPE--IEKGVEVVKHQKWSGATYIDGLLKMVSGGVTSTAAMGQGVTEDQ 480 ..|.||....|...--...|....|||...|..|.|.......||..||.||.......| query 384 RQMAAYSELQQAEFAAEADGYTATKHQREVGTGYFDAVSLAITGGQSSTTAMKESTETAQ 7EBE_A 548 FKESK 553 540 ||... 545 query 444 FKPAA 449 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [ [12, 60, 60, 75, 79, 99, 99, 157, 165, 274, 370, 504, 504, 553], [12, 60, 61, 76, 76, 96, 97, 155, 155, 264, 264, 398, 400, 449], ] ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), np.array( [ list(i) for i in [ "DIQKEEADFQKEVAEIKKWWSEPRWRKTKRIYSAEDIAKKRGTLKINH-PSSQQADKLFKLLEKHDADKTVSFTFGALDPIHVAQMAK-YLDSIYVSGWQCSSTASTSNEPSPDLADYPMDTVPNKVEHLWFAQLFHDRKQREERLTLSKEERAKTPYIDFLRPIIADADTGHGGITAIIKLTKMFIERGAAGIHIEDQAPGTKKCGHMAGKVLVPVQEHINRLVAIRASADIFGSNLLAVARTDSEAATLITSTIDHRDHYFIIGATNPEAGDLAALMAEAESKGIYGNELAAIESEWTKKAGLKLFHEAVIDEIKNGNYSNKDALIKKFTDKVNPLSHTSHKEAKKLAKELTGKDIYFNWDVARAREGYYRYQGGTQCAVMRGRAFAPYADLIWMESALPDYAQAKEFADGVKAAVPDQWLAYNLSPSFNWNKAMPADEQETYIKRLGKLGYVWQFITLAGLHTTALAVDDFSNQYSQIGMKAYGQTVQQPE--IEKGVEVVKHQKWSGATYIDGLLKMVSGGVTSTAAMGQGVTEDQFKESK", "EAQTQGPGSMTDFYSLIPSAPKGRFDGIERAHTAEDVKRLRGSVEIKYSLAEMGANRLWKLIHE----EDFVNALGALSGNQAMQMVRAGLKAIYLSGWQVAADANTASAMYPDQSLYPANAGPELAKRINRTLQRADQIETAEGKG--------LSVDTWFAPIVADAEAGFGGPLDAFEIMKAYIEAGAAGVHFEDQLASEKKCGHLGGKVLIPTAAHIRNLNAARLAADVMGTPTLIVARTDAEAAKLLTSDIDERDQPFV------------------------------------------------------------------------------------------------DYEAGRTAEGFYQVKNGIEPCIARAIAYAPYCDLIWMETSKPDLAQARRFAEAVHKAHPGKLLAYNCSPSFNWKKNLDDATIAKFQRELGAMGYKFQFITLAGFHQLNYGMFELARGYKDRQMAAYSELQQAEFAAEADGYTATKHQREVGTGYFDAVSLAITGGQSSTTAMKESTETAQFKPAA", ] ] ), ) ) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)